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Sample records for sp-d deficiency infers

  1. Linking surfactant protein SP-D and IL-13: implications in asthma and allergy.

    PubMed

    Qaseem, Asif S; Sonar, Sanchaita; Mahajan, Lakshna; Madan, Taruna; Sorensen, Grith L; Shamji, Mohamed H; Kishore, Uday

    2013-05-01

    Surfactant protein D (SP-D) is an innate immune molecule that plays a protective role against lung infection, allergy, asthma and inflammation. In vivo experiments with murine models have shown that SP-D can protect against allergic challenge via a range of mechanisms including inhibition of allergen-IgE interaction, histamine release by sensitised mast cells, downregulation of specific IgE production, suppression of pulmonary and peripheral eosinophilia, inhibition of mechanisms that cause airway remodelling, and induction of apoptosis in sensitised eosinophils. SP-D can also shift helper T cell polarisation following in vivo allergenic challenge, from pathogenic Th2 to a protective Th1 cytokine response. Interestingly, SP-D gene deficient (-/-) mice show an IL-13 over-expressing phenotype. IL-13 has been shown to be involved in the development of asthma. Transgenic mice over-expressing IL-13 in the lung develop several characteristics of asthma such as pulmonary eosinophilia, airway epithelial hyperplasia, mucus cell metaplasia, sub-epithelial fibrosis, charcot-Leyden-Like crystals, airways obstruction, and non-specific airways hyper-responsiveness to cholinergic stimulation. Although both IL-4 and IL-13 are capable of inducing asthma like phenotype, the effector activity of IL-13 appears to be greater than that of IL-4. SP-D -/- mice seem to express considerably higher levels of IL-13, which is consistent with increased sensitivity and exaggerated immune response of the mice to allergenic challenge. Allergenic exposure also induces elevation in SP-D protein levels in an IL-4/IL-13-dependent manner, which prevents further activation of sensitised T cells. This negative feedback loop seems essential in protecting the airways from inflammatory damage after allergen inhalation. Here, we examine this link between IL-13 and SP-D, and its implications in the progression/regulation of asthma and allergy. PMID:23220073

  2. Chronic obstructive pulmonary disease and inhaled steroids alter surfactant protein D (SP-D) levels: a cross-sectional study

    PubMed Central

    Sims, Michael W; Tal-Singer, Ruth M; Kierstein, Sonja; Musani, Ali I; Beers, Michael F; Panettieri, Reynold A; Haczku, Angela

    2008-01-01

    Background Surfactant protein D (SP-D), an innate immune molecule, plays an important protective role during airway inflammation. Deficiency of this molecule induces emphysematous changes in murine lungs, but its significance in human COPD remains unclear. Methods We collected bronchoalveolar lavage fluid from 20 subjects with varying degrees of COPD (8 former smokers and 12 current smokers) and 15 asymptomatic healthy control subjects (5 never smokers, 3 remote former smokers, and 7 current smokers). All subjects underwent a complete medical history and pulmonary function testing. SP-D was measured by Enzyme-Linked ImmunoSorbent Assay. Statistical analysis was performed using nonparametric methods and multivariable linear regression for control of confounding. The effect of corticosteroid treatment on SP-D synthesis was studied in vitro using an established model of isolated type II alveolar epithelial cell culture. Results Among former smokers, those with COPD had significantly lower SP-D levels than healthy subjects (median 502 and 1067 ng/mL, respectively, p = 0.01). In a multivariable linear regression model controlling for age, sex, race, and pack-years of tobacco, COPD was independently associated with lower SP-D levels (model coefficient -539, p = 0.04) and inhaled corticosteroid use was independently associated with higher SP-D levels (398, p = 0.046). To support the hypothesis that corticosteroids increase SP-D production we used type II alveolar epithelial cells isolated from adult rat lungs. These cells responded to dexamethasone treatment by a significant increase of SP-D mRNA (p = 0.041) and protein (p = 0.037) production after 4 days of culture. Conclusion Among former smokers, COPD is associated with lower levels of SP-D and inhaled corticosteroid use is associated with higher levels of SP-D in the lung. Dexamethasone induced SP-D mRNA and protein expression in isolated epithelial cells in vitro. Given the importance of this molecule as a modulator

  3. Gentisate 1,2-dioxygenase from Haloferax sp. D1227.

    PubMed

    Fu, W; Oriel, P

    1998-11-01

    Gentisate 1,2-dioxygenase from the extreme halophile Haloferax sp. D1227 (Hf. D1227) was purified using a three-step procedure. The enzyme was found to be a homotetramer of 42,000 +/- 1,000 Da subunits, with a native molecular weight of 174,000 +/- 6,000 Da. The optimal salt concentration, temperature, and pH for enzyme activity were 2 M KCl or NaCl, 45 degrees C, and pH 7.2, respectively. The gene encoding Hf. D1227 gentisate 1,2-dioxygenase was cloned, sequenced, and expressed in Haloferax volcanii. The deduced amino acid sequence exhibited a 9.2% excess acidic over basic amino acids typical of halophilic enzymes. Four novel histidine clusters and a possible extradiol dioxygenase fingerprint region were identified. PMID:9827334

  4. SP-D, KL-6, and HTI-56 levels in children with mycoplasma pneumoniae pneumonia

    PubMed Central

    Shu, Lin-Hua; Lu, Quan; Han, Li-Ying; Dong, Guang-Hui

    2015-01-01

    The study was aimed to evaluate the potential biomarkers from pulmonary surfactant protein D (SP-D), Krebs von den Lungen-6 (KL-6), and 56-kD a human type I protein (HTI-56) in serum and bronchoalveolar lavage fluid samples of children with Mycoplasma pneumoniae pneumonia. This retrospective study, self-controlled study enrolled 34 Chinese children with M. pneumoniae pneumonia. The levels of SP-D, KL-6, and HTI-56 in bronchoalveolar lavage fluid samples were assessed and compared between patients with unilateral lung infection and contralateral lungs without any abnormal findings. Significant differences in the levels of SP-D, KL-6, and HTI-56 were observed in infected bronchoalveolar lavage fluid samples compared with uninfected samples (all P<0.05); however, there was no correlation between the serum level of SP-D, KL-6, and HTI-56 and their levels in infected and uninfected bronchoalveolar lavage fluid samples (P>0.05). Conclusion: The high levels of SP-D, KL-6, and HTI-56 in infected bronchoalveolar lavage fluid samples may reflect the injury of alveolar epithelium caused by M. pneumoniae. Instead of SP-D in uninfected bronchoalveolar lavage fluid samples obtained by invasive bronchoscopy, serum SP-D may serve as a convenient medium to distinguish lung infection caused by M. pneumoniae. PMID:26617840

  5. Surfactant Protein D Deficiency in Mice Is Associated with Hyperphagia, Altered Fat Deposition, Insulin Resistance, and Increased Basal Endotoxemia

    PubMed Central

    Rahbek, Martin K. U.; Kirketerp-Møller, Katrine L.; Hansen, Pernille B. L.; Bie, Peter; Kejling, Karin; Mandrup, Susanne; Hawgood, Samuel; Nielsen, Ole; Nielsen, Claus H.; Owens, Trevor; Holmskov, Uffe; Sørensen, Grith L.

    2012-01-01

    Pulmonary surfactant protein D (SP-D) is a host defence lectin of the innate immune system that enhances clearance of pathogens and modulates inflammatory responses. Recently it has been found that systemic SP-D is associated with metabolic disturbances and that SP-D deficient mice are mildly obese. However, the mechanism behind SP-D's role in energy metabolism is not known. Here we report that SP-D deficient mice had significantly higher ad libitum energy intake compared to wild-type mice and unchanged energy expenditure. This resulted in accumulation but also redistribution of fat tissue. Blood pressure was unchanged. The change in energy intake was unrelated to the basal levels of hypothalamic Pro-opiomelanocortin (POMC) and Agouti-related peptide (AgRP) gene expression. Neither short time systemic, nor intracereberoventricular SP-D treatment altered the hypothalamic signalling or body weight accumulation. In ad libitum fed animals, serum leptin, insulin, and glucose were significantly increased in mice deficient in SP-D, and indicative of insulin resistance. However, restricted diets eliminated all metabolic differences except the distribution of body fat. SP-D deficiency was further associated with elevated levels of systemic bacterial lipopolysaccharide. In conclusion, our findings suggest that lack of SP-D mediates modulation of food intake not directly involving hypothalamic regulatory pathways. The resulting accumulation of adipose tissue was associated with insulin resistance. The data suggest SP-D as a regulator of energy intake and body composition and an inhibitor of metabolic endotoxemia. SP-D may play a causal role at the crossroads of inflammation, obesity, and insulin resistance. PMID:22509382

  6. Expression of surfactant proteins SP-A and SP-D in murine decidua and immunomodulatory effects on decidual macrophages.

    PubMed

    Madhukaran, Shanmuga Priyaa; Koippallil Gopalakrishnan, Aghila Rani; Pandit, Hrishikesh; Marri, Eswari Dodagatta-; Kouser, Lubna; Jamil, Kaiser; Alhamlan, Fatimah S; Kishore, Uday; Madan, Taruna

    2016-02-01

    Surfactant proteins SP-A and SP-D are pattern recognition innate immune molecules that belong to the C-type lectin family. In lungs, they play an important role in the clearance of pathogens and control of inflammation. SP-A and SP-D are also expressed in the female reproductive tract where they play an important role in pregnancy and parturition. However, the role of SP-A and SP-D expressed at the feto-maternal interface (decidua) remains unclear. Here, we have examined the expression of SP-A and SP-D in the murine decidua at 17.5 (pre-parturition) and 19.5dpc (near parturition) and their effect on lipopolysaccharide (LPS)-treated decidual macrophages. SP-A and SP-D were localized to stromal cells in the murine decidua at 17.5 and 19.5dpc in addition to cells lining the maternal spiral artery. Purified pre-parturition decidual cells were challenged with LPS with and without SP-A or SP-D, and expression of F4/80 and TNF-α were measured by flow cytometry. On their own, SP-A or SP-D did not affect the percentage of F4/80 positive cells while they suppressed the percentage of TNF-α positive cells. However, simultaneous addition of SP-A or SP-D, together with LPS, reduced TNF-α secreting F4/80 positive cells. It is likely that exogenous administration of SP-A and SP-D in decidua can potentially control infection and inflammation mediators during spontaneous term labor and infection-induced preterm labor. Thus, the presence of SP-A and SP-D in the murine decidua is likely to play a protective role against intrauterine infection during pregnancy. PMID:26421960

  7. Surfactant Proteins SP-A and SP-D Modulate Uterine Contractile Events in ULTR Myometrial Cell Line

    PubMed Central

    Sotiriadis, Georgios; Dodagatta-Marri, Eswari; Kouser, Lubna; Alhamlan, Fatimah S.; Kishore, Uday; Karteris, Emmanouil

    2015-01-01

    Pulmonary surfactant proteins SP-A and SP-D are pattern recognition innate immune molecules. However, there is extrapulmonary existence, especially in the amniotic fluid and at the feto-maternal interface. There is sufficient evidence to suggest that SP-A and SP-D are involved in the initiation of labour. This is of great importance given that preterm birth is associated with increased mortality and morbidity. In this study, we investigated the effects of recombinant forms of SP-A and SP-D (rhSP-A and rhSP-D, the comprising of trimeric lectin domain) on contractile events in vitro, using a human myometrial cell line (ULTR) as an experimental model. Treatment with rhSP-A or rhSP-D increased the cell velocity, distance travelled and displacement by ULTR cells. rhSP-A and rhSP-D also affected the contractile response of ULTRs when grown on collagen matrices showing reduced surface area. We investigated this effect further by measuring contractility-associated protein (CAP) genes. Treatment with rhSP-A and rhSP-D induced expression of oxytocin receptor (OXTR) and connexin 43 (CX43). In addition, rhSP-A and rhSP-D were able to induce secretion of GROα and IL-8. rhSP-D also induced the expression of IL-6 and IL-6 Ra. We provide evidence that SP-A and SP-D play a key role in modulating events prior to labour by reconditioning the human myometrium and in inducing CAP genes and pro-inflammatory cytokines thus shifting the uterus from a quiescent state to a contractile one. PMID:26641881

  8. Common Genetic Variants of Surfactant Protein-D (SP-D) Are Associated with Type 2 Diabetes

    PubMed Central

    Mercader, Josep M.; Moreno-Navarrete, José M.; Sabater, Monica; Bonàs, Sílvia; Botas, Patricia; Delgado, Elías; Ricart, Wifredo; Martinez-Larrad, María T.; Serrano-Ríos, Manuel; Torrents, David; Fernández-Real, José M.

    2013-01-01

    Context Surfactant protein-D (SP-D) is a primordial component of the innate immune system intrinsically linked to metabolic pathways. We aimed to study the association of single nucleotide polymorphisms (SNPs) affecting SP-D with insulin resistance and type 2 diabetes (T2D). Research Design and Methods We evaluated a common genetic variant located in the SP-D coding region (rs721917, Met31Thr) in a sample of T2D patients and non-diabetic controls (n = 2,711). In a subset of subjects (n = 1,062), this SNP was analyzed in association with circulating SP-D concentrations, insulin resistance, and T2D. This SNP and others were also screened in the publicly available Genome Wide Association (GWA) database of the Meta-Analyses of Glucose and Insulin-related traits Consortium (MAGIC). Results We found the significant association of rs721917 with circulating SP-D, parameters of insulin resistance and T2D. Indeed, G carriers showed decreased circulating SP-D (p = 0.004), decreased fasting glucose (p = 0.0002), glycated hemoglobin (p = 0.0005), and 33% (p = 0.002) lower prevalence of T2D, estimated under a dominant model, especially among women. Interestingly, these differences remained significant after controlling for origin, age, gender, and circulating SP-D. Moreover, this SNP and others within the SP-D genomic region (i.e. rs10887344) were significantly associated with quantitative measures of glucose homeostasis, insulin sensitivity, and T2D, according to GWAS datasets from MAGIC. Conclusions SP-D gene polymorphisms are associated with insulin resistance and T2D. These associations are independent of circulating SP-D concentrations. PMID:23577114

  9. Eutypenoids A–C: Novel Pimarane Diterpenoids from the Arctic Fungus Eutypella sp. D-1

    PubMed Central

    Zhang, Liu-Qiang; Chen, Xiao-Chong; Chen, Zhao-Qiang; Wang, Gui-Min; Zhu, Shi-Guo; Yang, Yi-Fu; Chen, Kai-Xian; Liu, Xiao-Yu; Li, Yi-Ming

    2016-01-01

    Eutypenoids A–C (1–3), pimarane diterpenoid alkaloid and two ring A rearranged pimarane diterpenoids, were isolated from the culture of Eutypella sp. D-1 obtained from high-latitude soil of the Arctic. Their structures, including absolute configurations, were authenticated on the basis of the mass spectroscopy (MS), nuclear magnetic resonance (NMR), X-ray crystallography, and electronic circular dichroism (ECD) analysis. The immunosuppressive effects of eutypenoids A–C (1–3) were studied using a ConA-induced splenocyte proliferation model, which suggested that 2 exhibited potent immunosuppressive activities. PMID:26959036

  10. Differences in serum SP-D levels between German and Japanese subjects are associated with SFTPD gene polymorphisms

    PubMed Central

    2014-01-01

    Background Surfactant protein A (SP-A) and SP-D are clinically established in Japan as serum biomarkers for diagnosing interstitial lung diseases (ILDs). Serum SP-D levels are affected by genetic variants. We conducted the present study to examine whether serum SP-A and/or SP-D levels in healthy subjects (HS) and patients with ILDs differ between populations with different genetic backgrounds. Methods German subjects (n = 303; 138 patients with idiopathic interstitial pneumonias [IIPs] and 165 HS) and Japanese subjects (n = 369; 94 patients with IIPs and 275 HS) were enrolled. Serum SP-A and SP-D levels were measured using an enzyme-linked immunosorbent assay, and four single-nucleotide polymorphisms (SNPs) in the SFTPD gene were genotyped using genomic DNA extracted from blood samples. Results In both the German and Japanese cohorts, serum SP-A and SP-D levels were significantly higher in patients with IIPs than in HS. There were no significant differences in SP-A levels between the German and Japanese cohorts; however, we found that serum SP-D levels were significantly higher in the German cohort, both in patients with IIPs and in HS (p < 0.001 and p = 0.005, respectively). Furthermore, the genotype distributions of the four SNPs in the SFTPD gene (rs721917, rs1998374, rs2243639, and rs3088308) were significantly different between German and Japanese cohorts (p < 0.001, p < 0.001, p = 0.022, and p < 0.001, respectively), and univariate linear regression analyses revealed that the genotypes of rs721917, rs1998374, and rs2243639 significantly correlated with serum SP-D levels (p < 0.001, p < 0.001, and p = 0.011, respectively). Furthermore, multivariate analyses revealed that the genotypes of these three SNPs correlated independently with serum SP-D levels (p < 0.001, p = 0.001, and p = 0.038, respectively), whereas ethnicity did not significantly correlate with serum SP-D levels. Conclusions In patients with IIPs and HS, serum SP-D, but

  11. Surfactant proteins, SP-A and SP-D, in respiratory fungal infections: their role in the inflammatory response.

    PubMed

    Carreto-Binaghi, Laura Elena; Aliouat, El Moukhtar; Taylor, Maria Lucia

    2016-01-01

    Pulmonary surfactant is a complex fluid that comprises phospholipids and four proteins (SP-A, SP-B, SP-C, and SP-D) with different biological functions. SP-B, SP-C, and SP-D are essential for the lungs' surface tension function and for the organization, stability and metabolism of lung parenchyma. SP-A and SP-D, which are also known as pulmonary collectins, have an important function in the host's lung immune response; they act as opsonins for different pathogens via a C-terminal carbohydrate recognition domain and enhance the attachment to phagocytic cells or show their own microbicidal activity by increasing the cellular membrane permeability. Interactions between the pulmonary collectins and bacteria or viruses have been extensively studied, but this is not the same for fungal pathogens. SP-A and SP-D bind glucan and mannose residues from fungal cell wall, but there is still a lack of information on their binding to other fungal carbohydrate residues. In addition, both their relation with immune cells for the clearance of these pathogens and the role of surfactant proteins' regulation during respiratory fungal infections remain unknown. Here we highlight the relevant findings associated with SP-A and SP-D in those respiratory mycoses where the fungal infective propagules reach the lungs by the airways. PMID:27250970

  12. SP-D counteracts GM-CSF-mediated increase of granuloma formation by alveolar macrophages in lysinuric protein intolerance

    PubMed Central

    2009-01-01

    Background Pulmonary alveolar proteinosis (PAP) is a syndrome with multiple etiologies and is often deadly in lysinuric protein intolerance (LPI). At present, PAP is treated by whole lung lavage or with granulocyte/monocyte colony stimulating factor (GM-CSF); however, the effectiveness of GM-CSF in treating LPI associated PAP is uncertain. We hypothesized that GM-CSF and surfactant protein D (SP-D) would enhance the clearance of proteins and dying cells that are typically present in the airways of PAP lungs. Methods Cells and cell-free supernatant of therapeutic bronchoalveolar lavage fluid (BALF) of a two-year-old patient with LPI were isolated on multiple occasions. Diagnostic BALF samples from an age-matched patient with bronchitis or adult PAP patients were used as controls. SP-D and total protein content of the supernatants were determined by BCA assays and Western blots, respectively. Cholesterol content was determined by a calorimetic assay or Oil Red O staining of cytospin preparations. The cells and surfactant lipids were also analyzed by transmission electron microscopy. Uptake of Alexa-647 conjugated BSA and DiI-labelled apoptotic Jurkat T-cells by BAL cells were studied separately in the presence or absence of SP-D (1 μg/ml) and/or GM-CSF (10 ng/ml), ex vivo. Specimens were analyzed by light and fluorescence microscopy. Results Here we show that large amounts of cholesterol, and large numbers of cholesterol crystals, dying cells, and lipid-laden foamy alveolar macrophages were present in the airways of the LPI patient. Although SP-D is present, its bioavailability is low in the airways. SP-D was partially degraded and entrapped in the unusual surfactant lipid tubules with circular lattice, in vivo. We also show that supplementing SP-D and GM-CSF increases the uptake of protein and dying cells by healthy LPI alveolar macrophages, ex vivo. Serendipitously, we found that these cells spontaneously generated granulomas, ex vivo, and GM-CSF treatment

  13. Ecological Inference

    NASA Astrophysics Data System (ADS)

    King, Gary; Rosen, Ori; Tanner, Martin A.

    2004-09-01

    This collection of essays brings together a diverse group of scholars to survey the latest strategies for solving ecological inference problems in various fields. The last half-decade has witnessed an explosion of research in ecological inference--the process of trying to infer individual behavior from aggregate data. Although uncertainties and information lost in aggregation make ecological inference one of the most problematic types of research to rely on, these inferences are required in many academic fields, as well as by legislatures and the Courts in redistricting, by business in marketing research, and by governments in policy analysis.

  14. Origin of magnetocrystalline anisotropy oscillations in (001) face-centred-cubic Co thin films and effect of sp d hybridization

    NASA Astrophysics Data System (ADS)

    Cinal, M.

    2003-01-01

    Magnetocrystalline anisotropy (MA) energy of (001) face-centred-cubic Co(N) films is calculated for film thicknesses N = 1-28 in a realistic tight-binding model with and without sp-d orbital hybridization included. The obtained results show that the average MA energy is not largely influenced by the sp-d hybridization. On the other hand, the oscillation pattern is remarkably changed when the sp-d hybridization is included: in this case the MA energy has oscillations with a clear period of 2 atomic layers (AL), similar to the previous ab initio calculations (Szunyogh L, Újfalussy B, Blaas C, Pustugova U, Sommers C and Weinberger P 1997 Phys. Rev. B 56 14036). A careful analysis in k- and N-spaces reveals that the total MA oscillations are a superposition of two oscillatory contributions: one coming from the neighbourhood of the barGamma-point with period close to 2 AL (regardless whether the sp-d hybridization is present or not) and the other originating in the region around the bar M-point. The bar M-point contribution has a larger period and its amplitude is significantly smaller than that of the barGamma-point contribution when the sp-d hybridization is included so that the 2 AL barGamma-point contribution is dominant in this case. The two oscillatory MA contributions are attributed to quantum-well states and the corresponding oscillation periods are related to the extremal radii of the minority-spin bulk Co Fermi surface.

  15. Humic substances increase survival of freshwater shrimp Caridina sp. D to acid mine drainage.

    PubMed

    Holland, Aleicia; Duivenvoorden, Leo J; Kinnear, Susan H W

    2013-02-01

    Humic substances (HS) are known to decrease the toxicity of heavy metals to aquatic organisms, and it has been suggested that they can provide buffering protection in low pH conditions. Despite this, little is known about the ability for HS to increase survival to acid mine drainage (AMD). In this study, the ability of HS to increase survival of the freshwater shrimp (Caridina sp. D sensu Page et al. in Biol Lett 1:139-142, 2005) to acid mine drainage was investigated using test waters collected from the Mount Morgan open pit in Central Queensland with the addition of Aldrich humic acid (AHA). The AMD water from the Mount Morgan open pit is highly acidic (pH 2.67) as well as contaminated with heavy metals (1780 mg/L aluminum, 101 mg/L copper [Cu], 173 mg/L manganese, 51.8 mg/L zinc [Zn], and 51.8 mg/L iron). Freshwater shrimp were exposed to dilutions in the range of 0.5 % to 5 % AMD water with and without the addition of 10 or 20 mg/L AHA. In the absence of HS, all shrimp died in the 2.5 % AMD treatment. In contrast, addition of HS increased survival in the 2.5 % AMD treatment by ≤66 % as well as significantly decreased the concentration of dissolved Cu, cobalt, cadmium, and Zn. The decreased toxicity of AMD in the presence of HS is likely to be due to complexation and precipitation of heavy metals with the HS; it is also possible that HS caused changes to the physiological condition of the shrimp, thus increasing their survival. These results are valuable in contributing to an improved understanding of potential role of HS in ameliorating the toxicity of AMD environments. PMID:23135152

  16. Entropic Inference

    NASA Astrophysics Data System (ADS)

    Caticha, Ariel

    2011-03-01

    In this tutorial we review the essential arguments behing entropic inference. We focus on the epistemological notion of information and its relation to the Bayesian beliefs of rational agents. The problem of updating from a prior to a posterior probability distribution is tackled through an eliminative induction process that singles out the logarithmic relative entropy as the unique tool for inference. The resulting method of Maximum relative Entropy (ME), includes as special cases both MaxEnt and Bayes' rule, and therefore unifies the two themes of these workshops—the Maximum Entropy and the Bayesian methods—into a single general inference scheme.

  17. Perceptual inference.

    PubMed

    Aggelopoulos, Nikolaos C

    2015-08-01

    Perceptual inference refers to the ability to infer sensory stimuli from predictions that result from internal neural representations built through prior experience. Methods of Bayesian statistical inference and decision theory model cognition adequately by using error sensing either in guiding action or in "generative" models that predict the sensory information. In this framework, perception can be seen as a process qualitatively distinct from sensation, a process of information evaluation using previously acquired and stored representations (memories) that is guided by sensory feedback. The stored representations can be utilised as internal models of sensory stimuli enabling long term associations, for example in operant conditioning. Evidence for perceptual inference is contributed by such phenomena as the cortical co-localisation of object perception with object memory, the response invariance in the responses of some neurons to variations in the stimulus, as well as from situations in which perception can be dissociated from sensation. In the context of perceptual inference, sensory areas of the cerebral cortex that have been facilitated by a priming signal may be regarded as comparators in a closed feedback loop, similar to the better known motor reflexes in the sensorimotor system. The adult cerebral cortex can be regarded as similar to a servomechanism, in using sensory feedback to correct internal models, producing predictions of the outside world on the basis of past experience. PMID:25976632

  18. Whole genome analysis of halotolerant and alkalotolerant plant growth-promoting rhizobacterium Klebsiella sp. D5A

    PubMed Central

    Liu, Wuxing; Wang, Qingling; Hou, Jinyu; Tu, Chen; Luo, Yongming; Christie, Peter

    2016-01-01

    This research undertook the systematic analysis of the Klebsiella sp. D5A genome and identification of genes that contribute to plant growth-promoting (PGP) traits, especially genes related to salt tolerance and wide pH adaptability. The genome sequence of isolate D5A was obtained using an Illumina HiSeq 2000 sequencing system with average coverages of 174.7× and 200.1× using the paired-end and mate-pair sequencing, respectively. Predicted and annotated gene sequences were analyzed for similarity with the Kyoto Encyclopedia of Genes and Genomes (KEGG) enzyme database followed by assignment of each gene into the KEGG pathway charts. The results show that the Klebsiella sp. D5A genome has a total of 5,540,009 bp with 57.15% G + C content. PGP conferring genes such as indole-3-acetic acid (IAA) biosynthesis, phosphate solubilization, siderophore production, acetoin and 2,3-butanediol synthesis, and N2 fixation were determined. Moreover, genes putatively responsible for resistance to high salinity including glycine-betaine synthesis, trehalose synthesis and a number of osmoregulation receptors and transport systems were also observed in the D5A genome together with numerous genes that contribute to pH homeostasis. These genes reveal the genetic adaptation of D5A to versatile environmental conditions and the effectiveness of the isolate to serve as a plant growth stimulator. PMID:27216548

  19. Whole genome analysis of halotolerant and alkalotolerant plant growth-promoting rhizobacterium Klebsiella sp. D5A.

    PubMed

    Liu, Wuxing; Wang, Qingling; Hou, Jinyu; Tu, Chen; Luo, Yongming; Christie, Peter

    2016-01-01

    This research undertook the systematic analysis of the Klebsiella sp. D5A genome and identification of genes that contribute to plant growth-promoting (PGP) traits, especially genes related to salt tolerance and wide pH adaptability. The genome sequence of isolate D5A was obtained using an Illumina HiSeq 2000 sequencing system with average coverages of 174.7× and 200.1× using the paired-end and mate-pair sequencing, respectively. Predicted and annotated gene sequences were analyzed for similarity with the Kyoto Encyclopedia of Genes and Genomes (KEGG) enzyme database followed by assignment of each gene into the KEGG pathway charts. The results show that the Klebsiella sp. D5A genome has a total of 5,540,009 bp with 57.15% G + C content. PGP conferring genes such as indole-3-acetic acid (IAA) biosynthesis, phosphate solubilization, siderophore production, acetoin and 2,3-butanediol synthesis, and N2 fixation were determined. Moreover, genes putatively responsible for resistance to high salinity including glycine-betaine synthesis, trehalose synthesis and a number of osmoregulation receptors and transport systems were also observed in the D5A genome together with numerous genes that contribute to pH homeostasis. These genes reveal the genetic adaptation of D5A to versatile environmental conditions and the effectiveness of the isolate to serve as a plant growth stimulator. PMID:27216548

  20. Testicular expression of SP-A, SP-D and MBL-A is positively regulated by testosterone and modulated by lipopolysaccharide.

    PubMed

    Rokade, Sushama; Madan, Taruna

    2016-09-01

    Pattern recognition proteins viz., Surfactant Protein-A (SP-A), Surfactant Protein-D (SP-D) and Mannan Binding Lectin-A (MBL-A) regulate inflammatory immune responses. In view of their plausible contribution to immune privilege in testis, the present study explored their expression and regulation in murine testis. The testicular expression of SP-A, SP-D and MBL-A significantly increased at puberty and was significantly down-regulated in testosterone suppression model. Of the isolated germ cells, Sertoli cells, myoid cells and Leydig cells, germ cells expressed SP-A, SP-D and MBL-A while myoid cells were found to express MBL-A. SP-A and SP-D were localised on head and tail of murine caudal sperm, whereas MBL-A was observed on the connecting piece and tail. Systemic lipopolysaccharide challenge significantly up-regulated SP-A and SP-D levels in murine testis after 24h. Positive regulation of collectins by testosterone and their modulation in response to inflammation implicates their involvement in testicular immune-privilege. PMID:27262512

  1. Genetic variant associations of human SP-A and SP-D with acute and chronic lung injury

    PubMed Central

    Silveyra, Patricia; Floros, Joanna

    2013-01-01

    Pulmonary surfactant, a lipoprotein complex, maintains alveolar integrity and plays an important role in lung host defense, and control of inflammation. Altered inflammatory processes and surfactant dysfunction are well described events that occur in patients with acute or chronic lung disease that can develop secondary to a variety of insults. Genetic variants of surfactant proteins, including single nucleotide polymorphisms, haplotypes, and other genetic variations have been associated with acute and chronic lung disease throughout life in several populations and study groups. The hydrophilic surfactant proteins SP-A and SP-D, also known as collectins, in addition to their surfactant-related functions, are important innate immunity molecules as these, among others, exhibit the ability to bind and enhance clearance of a wide range of pathogens and allergens. This review focuses on published association studies of human surfactant proteins A and D genetic polymorphisms with respiratory, and non-respiratory diseases in adults, children, and newborns. The potential role of genetic variations in pulmonary disease or pathogenesis is discussed following an evaluation, and comparison of the available literature. PMID:22201752

  2. Biological wastewater treatment of 1,4-dioxane using polyethylene glycol gel carriers entrapping Afipia sp. D1.

    PubMed

    Isaka, Kazuichi; Udagawa, Makiko; Kimura, Yuya; Sei, Kazunari; Ike, Michihiko

    2016-02-01

    A biological treatment system for 1,4-dioxane-containing wastewater was developed using the bacterium Afipia sp. D1, which can utilize 1,4-dioxane as the sole carbon source. Strain D1 was entrapped in a polyethylene glycol gel carrier to stably maintain it in a bioreactor, and continuous feeding tests were performed to treat model industrial wastewater containing 1,4-dioxane. 1,4-Dioxane removal activity rapidly increased soon after the start of feeding of influent with 400 mg/L 1,4-dioxane, and the volumetric removal rate reached 0.67 kg dioxane/m(3)/d on day 36 by a stepwise increase in loading. The start-up period of the 1,4-dioxane treatment reactor was approximately 1 month, and stable removal performance was subsequently achieved for more than 1 month. The average 1,4-dioxane effluent concentration and 1,4-dioxane removal efficiency were 3.6 mg/L and 99%, respectively, during stable operation. Further 1,4-dioxane degradation activity of the of the gel carrier was characterized in batch experiments with respect to temperature. The optimum temperature for 1,4-dioxane treatment was 31.7°C, and significant removal was observed at a temperature as low as 6.9°C. The apparent activation energy for 1,4-dioxane degradation was estimated to be 47.3 kJ/mol. This is the first report of the development of a 1,4-dioxane biological treatment system using gel entrapment technology. PMID:26168905

  3. Biodegradation of chlorimuron-ethyl and the associated degradation pathway by Rhodococcus sp. D310-1.

    PubMed

    Li, Chunyan; Zang, Hailian; Yu, Qi; Lv, Tongyang; Cheng, Yi; Cheng, Xiaosong; Liu, Keran; Liu, Wanjun; Xu, Pianpian; Lan, Chuanzeng

    2016-05-01

    Chlorimuron-ethyl is a typical long-term residual sulfonylurea herbicide, and strategies for its removal have attracted increasing attention. Microbial degradation is considered the most acceptable dissipation method. In this study, we optimized the cultivation conditions (substrate concentration, pH, inoculum concentration, and temperature) of the chlorimuron-ethyl-degrading bacterium Rhodococcus sp. D310-1 using response surface methodology (RSM) to improve the biodegradation efficiency. A maximum biodegradation rate of 88.95 % was obtained. The Andrews model was used to describe the changes in the specific degradation rate as the substrate concentration increased. Chlorimuron-ethyl could be transformed with a maximum specific degradation rate (q max), half-saturation constant (K S), and inhibition constant (K i) of 0.4327 day(-1), 63.50045 mg L(-1), and 156.76666 mg L(-1), respectively. Eight biodegradation products (2-amino-4-chloro-6-methoxypyrimidine, ethyl 2-sulfamoyl benzoate, 2-sulfamoyl benzoic acid, o-benzoic sulfimide, 2-[[(4-chloro-6-methoxy-2-pyrimidinyl) carbamoyl] sulfamoyl] benzoic acid, ethyl 2-carbonyl sulfamoyl benzoate, ethyl 2-benzenesulfonyl isocyanate benzoate, and N,N-2(ethyl formate)benzene sulfonylurea) were identified, and three possible degradation pathways were proposed based on the results of high performance liquid chromatography HPLC, liquid chromatography tandem mass spectroscopy (LC-MS/MS), and Fourier transform infrared spectroscopy (FTIR) analyses and the relevant literature. This systematic study is the first to examine the chlorimuron-ethyl degradation pathways of the genus Rhodococcus. PMID:26810662

  4. Combined remediation of DDT congeners and cadmium in soil by Sphingobacterium sp. D-6 and Sedum alfredii Hance.

    PubMed

    Fang, Hua; Zhou, Wei; Cao, Zhengya; Tang, Feifan; Wang, Dandan; Liu, Kailin; Wu, Xiangwei; Yang, Xiao'e; Sun, Yongge; Yu, Yunlong

    2012-01-01

    Combined pollution of 1,1,1-trichloro-2,2-bis (4-chlorophenyl) ethane (DDT) and cadmium (Cd) in agricultural soils is of great concern because they present serious risk to food security and human health. In order to develop a cost-effective and safe method for the removal of DDTs and Cd in soil, combined remediation of DDTs and Cd in soil by Sphingobacterium sp. D-6 and the hyperaccumulator, Sedum alfredii Hance was investigated. After treatment for 210 days, the degradation half-lives of DDTs in soils treated by strain D-6 decreased by 8.1% to 68.0% compared with those in the controls. The inoculation of strain D-6 into soil decreased the uptake of DDTs by pak choi and S. alfredii. The shoots/roots ratios of S. alfredii for the Cd accumulation ranged from 12.32 to 21.75. The Cd concentration in soil decreased to 65.8%-71.8% for S. alfredii treatment and 14.1%-58.2% for S. alfredii and strain D-6 combined treatment, respectively, compared with that in the control. The population size of the DDTs-degrading strain, Simpson index (1/D) and soil respiratory rate decreased in the early stage of treatment and then gradually increased, ultimately recovering to or exceeding the initial level. The results indicated that synchronous incorporation of strain D-6 and S. alfredii into soil was found to significantly (p < or = 0.05) enhance the degradation of DDTs in soil and the hyperaccumulation of Cd in S. alfredii. It was concluded that strain D-6 and S. alfredii could be used successfully to control DDTs and Cd in contaminated soil. PMID:23505871

  5. Comparative Study of Circulating MMP-7, CCL18, KL-6, SP-A, and SP-D as Disease Markers of Idiopathic Pulmonary Fibrosis.

    PubMed

    Hamai, Kosuke; Iwamoto, Hiroshi; Ishikawa, Nobuhisa; Horimasu, Yasushi; Masuda, Takeshi; Miyamoto, Shintaro; Nakashima, Taku; Ohshimo, Shinichiro; Fujitaka, Kazunori; Hamada, Hironobu; Hattori, Noboru; Kohno, Nobuoki

    2016-01-01

    Background. Recent reports indicate that matrix metalloproteinase-7 (MMP-7) and CC-chemokine ligand 18 (CCL18) are potential disease markers of idiopathic pulmonary fibrosis (IPF). The objective of this study was to perform direct comparisons of these two biomarkers with three well-investigated serum markers of IPF, Krebs von den Lungen-6 (KL-6), surfactant protein-A (SP-A), and SP-D. Methods. The serum levels of MMP-7, CCL18, KL-6, SP-A, and SP-D were evaluated in 65 patients with IPF, 31 patients with bacterial pneumonia, and 101 healthy controls. The prognostic performance of these five biomarkers was evaluated in patients with IPF. Results. The serum levels of MMP-7, KL-6, and SP-D in patients with IPF were significantly elevated compared to those in patients with bacterial pneumonia and in the healthy controls. Multivariate survival analysis showed that serum MMP-7 and KL-6 levels were independent predictors in IPF patients. Moreover, elevated levels of both KL-6 and MMP-7 were associated with poorer survival rates in IPF patients, and the combination of both markers provided the best risk discrimination using the C statistic. Conclusions. The present results indicated that MMP-7 and KL-6 were promising prognostic markers of IPF, and the combination of the two markers might improve survival prediction in patients with IPF. PMID:27293304

  6. Comparative Study of Circulating MMP-7, CCL18, KL-6, SP-A, and SP-D as Disease Markers of Idiopathic Pulmonary Fibrosis

    PubMed Central

    Hamai, Kosuke; Iwamoto, Hiroshi; Ishikawa, Nobuhisa; Horimasu, Yasushi; Masuda, Takeshi; Miyamoto, Shintaro; Nakashima, Taku; Ohshimo, Shinichiro; Fujitaka, Kazunori; Hamada, Hironobu; Hattori, Noboru; Kohno, Nobuoki

    2016-01-01

    Background. Recent reports indicate that matrix metalloproteinase-7 (MMP-7) and CC-chemokine ligand 18 (CCL18) are potential disease markers of idiopathic pulmonary fibrosis (IPF). The objective of this study was to perform direct comparisons of these two biomarkers with three well-investigated serum markers of IPF, Krebs von den Lungen-6 (KL-6), surfactant protein-A (SP-A), and SP-D. Methods. The serum levels of MMP-7, CCL18, KL-6, SP-A, and SP-D were evaluated in 65 patients with IPF, 31 patients with bacterial pneumonia, and 101 healthy controls. The prognostic performance of these five biomarkers was evaluated in patients with IPF. Results. The serum levels of MMP-7, KL-6, and SP-D in patients with IPF were significantly elevated compared to those in patients with bacterial pneumonia and in the healthy controls. Multivariate survival analysis showed that serum MMP-7 and KL-6 levels were independent predictors in IPF patients. Moreover, elevated levels of both KL-6 and MMP-7 were associated with poorer survival rates in IPF patients, and the combination of both markers provided the best risk discrimination using the C statistic. Conclusions. The present results indicated that MMP-7 and KL-6 were promising prognostic markers of IPF, and the combination of the two markers might improve survival prediction in patients with IPF. PMID:27293304

  7. Immobilization of Erwinia sp. D12 Cells in Alginate-Gelatin Matrix and Conversion of Sucrose into Isomaltulose Using Response Surface Methodology

    PubMed Central

    Kawaguti, Haroldo Yukio; Carvalho, Priscila Hoffmann; Figueira, Joelise Alencar; Sato, Hélia Harumi

    2011-01-01

    Isomaltulose is a noncariogenic reducing disaccharide and also a structural isomer of sucrose and is used by the food industry as a sucrose replacement. It is obtained through enzymatic conversion of microbial sucrose isomerase. An Erwinia sp. D12 strain is capable of converting sucrose into isomaltulose. The experimental design technique was used to study the influence of immobilization parameters on converting sucrose into isomaltulose in a batch process using shaken Erlenmeyer flasks. We assessed the effect of gelatin and transglutaminase addition on increasing the reticulation of granules of Erwinia sp. D12 cells immobilized in alginate. Independent parameters, sodium alginate concentration, cell mass concentration, CaCl2 concentration, gelatin concentration, and transglutaminase concentration had all a significant effect (P < 0.05) on isomaltulose production. Erwinia sp. D12 cells immobilized in 3.0% (w/v) sodium alginate, 47.0% (w/v) cell mass, 0.3 molL−1 CaCl2, 1.7% (w/v) gelatin and 0.15% (w/v) transglutaminase presented sucrose conversion into isomaltulose, of around 50–60% in seven consecutive batches. PMID:21785708

  8. Iron deficiency.

    PubMed

    Scrimshaw, N S

    1991-10-01

    The world's leading nutritional problem is iron deficiency. 66% of children and women aged 15-44 years in developing countries have it. Further, 10-20% of women of childbearing age in developed countries are anemic. Iron deficiency is identified with often irreversible impairment of a child's learning ability. It is also associated with low capacity for adults to work which reduces productivity. In addition, it impairs the immune system which reduces the body's ability to fight infection. Iron deficiency also lowers the metabolic rate and the body temperature when exposed to cold. Hemoglobin contains nearly 73% of the body's iron. This iron is always being recycled as more red blood cells are made. The rest of the needed iron does important tasks for the body, such as binds to molecules that are reservoirs of oxygen for muscle cells. This iron comes from our diet, especially meat. Even though some plants, such as spinach, are high in iron, the body can only absorb 1.4-7% of the iron in plants whereas it can absorb 20% of the iron in red meat. In many developing countries, the common vegetarian diets contribute to high rates of iron deficiency. Parasitic diseases and abnormal uterine bleeding also promote iron deficiency. Iron therapy in anemic children can often, but not always, improve behavior and cognitive performance. Iron deficiency during pregnancy often contributes to maternal and perinatal mortality. Yet treatment, if given to a child in time, can lead to normal growth and hinder infections. However, excess iron can be damaging. Too much supplemental iron in a malnourished child promotes fatal infections since the excess iron is available for the pathogens use. Many countries do not have an effective system for diagnosing, treating, and preventing iron deficiency. Therefore a concerted international effort is needed to eliminate iron deficiency in the world. PMID:1745900

  9. Inference or Observation?

    ERIC Educational Resources Information Center

    Finson, Kevin D.

    2010-01-01

    Learning about what inferences are, and what a good inference is, will help students become more scientifically literate and better understand the nature of science in inquiry. Students in K-4 should be able to give explanations about what they investigate (NSTA 1997) and that includes doing so through inferring. This article provides some tips…

  10. The importance of light and photoperiod in sexual reproduction and geographical distribution in the green snow alga, Chloromonas sp.-D (Chlorophyceae, Volvocales)

    NASA Astrophysics Data System (ADS)

    Hoham, Ronald W.; Marcarelli, Amy M.; Rogers, Haldre S.; Ragan, Michael D.; Petre, Benjamin M.; Ungerer, Michael D.; Barnes, Joseph M.; Francis, David O.

    2000-12-01

    The effects of premating light regimes on sexual reproduction and the production of spherical cells in Chloromonas sp.-D, a unicellular green snow alga, were studied using cross-mating strains 582C and 582D isolated from snowpacks associated with mixed hardwood- softwood forests in Whetstone Gulf State Park, Tughill Plateau, NY. Two pre-acclimation regimes were used, Vita-Lite as controls (530- 700 nm peak) and blue light as experimentals (430- 460 nm peak) prior to the mating experiments. In blue light, an increase in the number of matings and spherical cells (spheres) produced in the life cycle was observed as the photoperiod increased. This implies that longer photoperiods of blue light are more optimal for sexual reproduction in Chloromonas sp.-D than shorter ones. Under Vita-Lite, there was a significant increase in the number of matings and spheres with the extended 20 : 4 photoperiod compared with the shorter 14 : 10 photoperiod. Under blue light, significantly more matings and spheres occurred than under Vita-Lite using the same irradiance level of 95µmol photons m-2 s-1 (photosynthetically active radiation [PAR] of 400- 700 nm) for the 14 : 10 and 20 : 4 photoperiods. The results of these experiments suggest that Chloromonas sp.-D, known only from the Tughill Plateau, NY, is not reproducing optimally at this site where it grows and reproduces under an approximate 14 : 10 photoperiod in early April. However, in the upper 10 cm of snow in the Tughill Plateau, a blue light irradiance level of 95µmol photons m-2 s-1 occurs, which is optimal for this species. When these conditions are combined with a 14 : 10 photoperiod, the Tughill Plateau appears to be sub-optimal for mating and production of spherical cells. Since Chloromonas sp.-D does not appear to have a dependence on a dark cycle, this would allow it to expand its geographical distribution. It may reproduce more optimally under blue light (95µmol photons m-2 s-1) with an extended photoperiod (>20 : 4

  11. High resolution mass spectrometric alveolar proteomics: identification of surfactant protein SP-A and SP-D modifications in proteinosis and cystic fibrosis patients.

    PubMed

    Bai, Yu; Galetskiy, Dmitry; Damoc, Eugen; Paschen, Christian; Liu, Zhiqiang; Griese, Mathias; Liu, Shuying; Przybylski, Michael

    2004-08-01

    In the present study, one- and two-dimensional gel electrophoresis combined with high resolution Fourier transform-ion cyclotron resonance mass spectrometry (FT-ICR MS) have been applied as powerful approaches for the proteome analysis of surfactant proteins SP-A and SP-D, including identification of structurally modified and truncation forms, in bronchoalveolar lavage fluid from patients with cystic fibrosis, chronic bronchitis and pulmonary alveolar proteinosis. Highly sensitive micropreparation techniques were developed for matrix-assisted laser desorption/ionization (MALDI) FT-ICR MS analysis which provided the identification of surfactant proteins at very low levels. Owing to the high resolution, FT-ICR MS was found to provide substantial advantages for the structural identification of surfactant proteins from complex biological matrices with high mass determination accuracy. Several protein bands corresponding to SP-A and SP-D were identified by MALDI-FT-ICR MS after electrophoretic separation by one- and two-dimensional gel electrophoresis, and provided the identification of structural modifications (hydroxy-proline) and degradation products. The high resolution mass spectrometric proteome analysis should facilitate the unequivocal identification of subunits, aggregations, modifications and degradation products of surfactant proteins and hence contribute to the understanding of the mechanistic basis of lung disease pathogenesis. PMID:15274124

  12. Physical limits of inference

    NASA Astrophysics Data System (ADS)

    Wolpert, David H.

    2008-07-01

    We show that physical devices that perform observation, prediction, or recollection share an underlying mathematical structure. We call devices with that structure “inference devices”. We present a set of existence and impossibility results concerning inference devices. These results hold independent of the precise physical laws governing our universe. In a limited sense, the impossibility results establish that Laplace was wrong to claim that even in a classical, non-chaotic universe the future can be unerringly predicted, given sufficient knowledge of the present. Alternatively, these impossibility results can be viewed as a non-quantum-mechanical “uncertainty principle”. The mathematics of inference devices has close connections to the mathematics of Turing Machines (TMs). In particular, the impossibility results for inference devices are similar to the Halting theorem for TMs. Furthermore, one can define an analog of Universal TMs (UTMs) for inference devices. We call those analogs “strong inference devices”. We use strong inference devices to define the “inference complexity” of an inference task, which is the analog of the Kolmogorov complexity of computing a string. A task-independent bound is derived on how much the inference complexity of an inference task can differ for two different inference devices. This is analogous to the “encoding” bound governing how much the Kolmogorov complexity of a string can differ between two UTMs used to compute that string. However no universe can contain more than one strong inference device. So whereas the Kolmogorov complexity of a string is arbitrary up to specification of the UTM, there is no such arbitrariness in the inference complexity of an inference task. We informally discuss the philosophical implications of these results, e.g., for whether the universe “is” a computer. We also derive some graph-theoretic properties governing any set of multiple inference devices. We also present an

  13. Alpha-1 Antitrypsin Deficiency

    MedlinePlus

    ... Liver Disease Information > Alpha-1 Antitrypsin Deficiency Alpha-1 Antitrypsin Deficiency Explore this section to learn more about alpha-1 antitrypsin deficiency, including a description of the disorder ...

  14. Inference in `poor` languages

    SciTech Connect

    Petrov, S.

    1996-10-01

    Languages with a solvable implication problem but without complete and consistent systems of inference rules (`poor` languages) are considered. The problem of existence of finite complete and consistent inference rule system for a ``poor`` language is stated independently of the language or rules syntax. Several properties of the problem arc proved. An application of results to the language of join dependencies is given.

  15. Identification of the Antibacterial Compound Produced by the Marine Epiphytic Bacterium Pseudovibrio sp. D323 and Related Sponge-Associated Bacteria

    PubMed Central

    Penesyan, Anahit; Tebben, Jan; Lee, Matthew; Thomas, Torsten; Kjelleberg, Staffan; Harder, Tilmann; Egan, Suhelen

    2011-01-01

    Surface-associated marine bacteria often produce secondary metabolites with antagonistic activities. In this study, tropodithietic acid (TDA) was identified to be responsible for the antibacterial activity of the marine epiphytic bacterium Pseudovibrio sp. D323 and related strains. Phenol was also produced by these bacteria but was not directly related to the antibacterial activity. TDA was shown to effectively inhibit a range of marine bacteria from various phylogenetic groups. However TDA-producers themselves were resistant and are likely to possess resistance mechanism preventing autoinhibition. We propose that TDA in isolate D323 and related eukaryote-associated bacteria plays a role in defending the host organism against unwanted microbial colonisation and, possibly, bacterial pathogens. PMID:21892353

  16. Temporal stability of parasite distribution and genetic variability values of Contracaecum osculatum sp. D and C. osculatum sp. E (Nematoda: Anisakidae) from fish of the Ross Sea (Antarctica)

    PubMed Central

    Mattiucci, Simonetta; Cipriani, Paolo; Paoletti, Michela; Nardi, Valentina; Santoro, Mario; Bellisario, Bruno; Nascetti, Giuseppe

    2015-01-01

    The Ross Sea, Eastern Antarctica, is considered a “pristine ecosystem” and a biodiversity “hotspot” scarcely impacted by humans. The sibling species Contracaecum osculatum sp. D and C. osculatum sp. E are anisakid parasites embedded in the natural Antarctic marine ecosystem. Aims of this study were to: identify the larvae of C. osculatum (s.l.) recovered in fish hosts during the XXVII Italian Expedition to Antarctica (2011–2012); perform a comparative analysis of the contemporary parasitic load and genetic variability estimates of C. osculatum sp. D and C. osculatum sp. E with respect to samples collected during the expedition of 1993–1994; to provide ecological data on these parasites. 200 fish specimens (Chionodraco hamatus, Trematomus bernacchii, Trematomus hansoni, Trematomus newnesi) were analysed for Contracaecum sp. larvae, identified at species level by allozyme diagnostic markers and sequences analysis of the mtDNA cox2 gene. Statistically significant differences were found between the occurrence of C. osculatum sp. D and C. osculatum sp. E in different fish species. C. osculatum sp. E was more prevalent in T. bernacchii; while, a higher percentage of C. osculatum sp. D occurred in Ch. hamatus and T. hansoni. The two species also showed differences in the host infection site: C. osculatum sp. D showed higher percentage of infection in the fish liver. High genetic variability values at both nuclear and mitochondrial level were found in the two species in both sampling periods. The parasitic infection levels by C. osculatum sp. D and sp. E and their estimates of genetic variability showed no statistically significant variation over a temporal scale (2012 versus 1994). This suggests that the low habitat disturbance of the Antarctic region permits the maintenance of stable ecosystem trophic webs, which contributes to the maintenance of a large populations of anisakid nematodes with high genetic variability. PMID:26767164

  17. PGK deficiency.

    PubMed

    Beutler, Ernest

    2007-01-01

    Phosphoglycerate kinase (PGK) deficiency is one of the relatively uncommon causes of hereditary non-spherocytic haemolytic anaemia (HNSHA). The gene encoding the erythrocyte enzyme PGK1, is X-linked. Mutations of this gene may cause chronic haemolysis with or without mental retardation and they may cause myopathies, often with episodes of myoglobinuria, or a combination of these clinical manifestations. Twenty-six families have been described and in 20 of these the mutations are known. The reason for different clinical manifestations of mutations of the same gene remains unknown. PMID:17222195

  18. The Bayes Inference Engine

    SciTech Connect

    Hanson, K.M.; Cunningham, G.S.

    1996-04-01

    The authors are developing a computer application, called the Bayes Inference Engine, to provide the means to make inferences about models of physical reality within a Bayesian framework. The construction of complex nonlinear models is achieved by a fully object-oriented design. The models are represented by a data-flow diagram that may be manipulated by the analyst through a graphical programming environment. Maximum a posteriori solutions are achieved using a general, gradient-based optimization algorithm. The application incorporates a new technique of estimating and visualizing the uncertainties in specific aspects of the model.

  19. INFERENCES FROM ROSSI TRACES

    SciTech Connect

    KENNETH M. HANSON; JANE M. BOOKER

    2000-09-08

    The authors an uncertainty analysis of data taken using the Rossi technique, in which the horizontal oscilloscope sweep is driven sinusoidally in time ,while the vertical axis follows the signal amplitude. The analysis is done within a Bayesian framework. Complete inferences are obtained by tilting the Markov chain Monte Carlo technique, which produces random samples from the posterior probability distribution expressed in terms of the parameters.

  20. Zeeman Splitting Caused by Localized sp-d Exchange Interaction in Ferromagnetic GaMnAs Observed by Magneto-Optical Characterization

    NASA Astrophysics Data System (ADS)

    Tanaka, Hiroki

    .97Mn0.03As measured at 6 K. To calculate the Zeeman splitting energy at E0 (Gamma-CP), an experimentally reported parameter of a II-VI paramagnetic DMS, Cd 1-xMnxTe, was used due to some similarities of their electronic band structure. The Zeeman splitting energy at E0 (Gamma-CP) of Ga0.97Mn0.03As on sapphire, Ga 0.97Mn0.03As on InP, and free-standing Ga0.97Mn 0.03As was ~ 64 meV, ~ 9.6, meV and ~ 104 meV at 6 K. In addition, we found that MCD spectra around L-critical points shifted toward lower energy whereas the corresponding absorption spectra did not shift toward lower energy with an increase of Mn concentration. These results indicate that the sp-d exchange interaction in Ga1-xMn xAs has a very localized nature, because MCD is only active in a region where a band structure is affected by Mn spins, and optical absorption results from the overall sample response. This means that the sp-d exchange interactions are only generated within the sphere of influence.

  1. Active inference and learning.

    PubMed

    Friston, Karl; FitzGerald, Thomas; Rigoli, Francesco; Schwartenbeck, Philipp; O'Doherty, John; Pezzulo, Giovanni

    2016-09-01

    This paper offers an active inference account of choice behaviour and learning. It focuses on the distinction between goal-directed and habitual behaviour and how they contextualise each other. We show that habits emerge naturally (and autodidactically) from sequential policy optimisation when agents are equipped with state-action policies. In active inference, behaviour has explorative (epistemic) and exploitative (pragmatic) aspects that are sensitive to ambiguity and risk respectively, where epistemic (ambiguity-resolving) behaviour enables pragmatic (reward-seeking) behaviour and the subsequent emergence of habits. Although goal-directed and habitual policies are usually associated with model-based and model-free schemes, we find the more important distinction is between belief-free and belief-based schemes. The underlying (variational) belief updating provides a comprehensive (if metaphorical) process theory for several phenomena, including the transfer of dopamine responses, reversal learning, habit formation and devaluation. Finally, we show that active inference reduces to a classical (Bellman) scheme, in the absence of ambiguity. PMID:27375276

  2. Bayesian inference in physics

    NASA Astrophysics Data System (ADS)

    von Toussaint, Udo

    2011-07-01

    Bayesian inference provides a consistent method for the extraction of information from physics experiments even in ill-conditioned circumstances. The approach provides a unified rationale for data analysis, which both justifies many of the commonly used analysis procedures and reveals some of the implicit underlying assumptions. This review summarizes the general ideas of the Bayesian probability theory with emphasis on the application to the evaluation of experimental data. As case studies for Bayesian parameter estimation techniques examples ranging from extra-solar planet detection to the deconvolution of the apparatus functions for improving the energy resolution and change point estimation in time series are discussed. Special attention is paid to the numerical techniques suited for Bayesian analysis, with a focus on recent developments of Markov chain Monte Carlo algorithms for high-dimensional integration problems. Bayesian model comparison, the quantitative ranking of models for the explanation of a given data set, is illustrated with examples collected from cosmology, mass spectroscopy, and surface physics, covering problems such as background subtraction and automated outlier detection. Additionally the Bayesian inference techniques for the design and optimization of future experiments are introduced. Experiments, instead of being merely passive recording devices, can now be designed to adapt to measured data and to change the measurement strategy on the fly to maximize the information of an experiment. The applied key concepts and necessary numerical tools which provide the means of designing such inference chains and the crucial aspects of data fusion are summarized and some of the expected implications are highlighted.

  3. Towards Context Sensitive Information Inference.

    ERIC Educational Resources Information Center

    Song, D.; Bruza, P. D.

    2003-01-01

    Discusses information inference from a psychologistic stance and proposes an information inference mechanism that makes inferences via computations of information flow through an approximation of a conceptual space. Highlights include cognitive economics of information processing; context sensitivity; and query models for information retrieval.…

  4. Visual Inference Programming

    NASA Technical Reports Server (NTRS)

    Wheeler, Kevin; Timucin, Dogan; Rabbette, Maura; Curry, Charles; Allan, Mark; Lvov, Nikolay; Clanton, Sam; Pilewskie, Peter

    2002-01-01

    The goal of visual inference programming is to develop a software framework data analysis and to provide machine learning algorithms for inter-active data exploration and visualization. The topics include: 1) Intelligent Data Understanding (IDU) framework; 2) Challenge problems; 3) What's new here; 4) Framework features; 5) Wiring diagram; 6) Generated script; 7) Results of script; 8) Initial algorithms; 9) Independent Component Analysis for instrument diagnosis; 10) Output sensory mapping virtual joystick; 11) Output sensory mapping typing; 12) Closed-loop feedback mu-rhythm control; 13) Closed-loop training; 14) Data sources; and 15) Algorithms. This paper is in viewgraph form.

  5. Circular inferences in schizophrenia.

    PubMed

    Jardri, Renaud; Denève, Sophie

    2013-11-01

    A considerable number of recent experimental and computational studies suggest that subtle impairments of excitatory to inhibitory balance or regulation are involved in many neurological and psychiatric conditions. The current paper aims to relate, specifically and quantitatively, excitatory to inhibitory imbalance with psychotic symptoms in schizophrenia. Considering that the brain constructs hierarchical causal models of the external world, we show that the failure to maintain the excitatory to inhibitory balance results in hallucinations as well as in the formation and subsequent consolidation of delusional beliefs. Indeed, the consequence of excitatory to inhibitory imbalance in a hierarchical neural network is equated to a pathological form of causal inference called 'circular belief propagation'. In circular belief propagation, bottom-up sensory information and top-down predictions are reverberated, i.e. prior beliefs are misinterpreted as sensory observations and vice versa. As a result, these predictions are counted multiple times. Circular inference explains the emergence of erroneous percepts, the patient's overconfidence when facing probabilistic choices, the learning of 'unshakable' causal relationships between unrelated events and a paradoxical immunity to perceptual illusions, which are all known to be associated with schizophrenia. PMID:24065721

  6. Moment inference from tomograms

    USGS Publications Warehouse

    Day-Lewis, F. D.; Chen, Y.; Singha, K.

    2007-01-01

    Time-lapse geophysical tomography can provide valuable qualitative insights into hydrologic transport phenomena associated with aquifer dynamics, tracer experiments, and engineered remediation. Increasingly, tomograms are used to infer the spatial and/or temporal moments of solute plumes; these moments provide quantitative information about transport processes (e.g., advection, dispersion, and rate-limited mass transfer) and controlling parameters (e.g., permeability, dispersivity, and rate coefficients). The reliability of moments calculated from tomograms is, however, poorly understood because classic approaches to image appraisal (e.g., the model resolution matrix) are not directly applicable to moment inference. Here, we present a semi-analytical approach to construct a moment resolution matrix based on (1) the classic model resolution matrix and (2) image reconstruction from orthogonal moments. Numerical results for radar and electrical-resistivity imaging of solute plumes demonstrate that moment values calculated from tomograms depend strongly on plume location within the tomogram, survey geometry, regularization criteria, and measurement error. Copyright 2007 by the American Geophysical Union.

  7. Folate-deficiency anemia

    MedlinePlus

    ... medlineplus.gov/ency/article/000551.htm Folate-deficiency anemia To use the sharing features on this page, please enable JavaScript. Folate-deficiency anemia is a decrease in red blood cells (anemia) ...

  8. Alpha-1 Antitrypsin Deficiency

    MedlinePlus

    ... from the NHLBI on Twitter. What Is Alpha-1 Antitrypsin Deficiency? Alpha-1 antitrypsin (an-tee-TRIP-sin) deficiency, or AAT ... as it relates to lung disease. Overview Alpha-1 antitrypsin, also called AAT, is a protein made ...

  9. DOCK8 Deficiency

    MedlinePlus

    ... on ClinicalTrials.gov . Related Links Primary Immune Deficiency Diseases (PIDDs) Immune System ​​​​​​​ Javascript Error Your browser JavaScript is turned ... Scientists Identify Genetic Cause of Previously Undefined Primary Immune Deficiency Disease Signs and Symptoms DOCK8 deficiency causes persistent skin ...

  10. BIE: Bayesian Inference Engine

    NASA Astrophysics Data System (ADS)

    Weinberg, Martin D.

    2013-12-01

    The Bayesian Inference Engine (BIE) is an object-oriented library of tools written in C++ designed explicitly to enable Bayesian update and model comparison for astronomical problems. To facilitate "what if" exploration, BIE provides a command line interface (written with Bison and Flex) to run input scripts. The output of the code is a simulation of the Bayesian posterior distribution from which summary statistics e.g. by taking moments, or determine confidence intervals and so forth, can be determined. All of these quantities are fundamentally integrals and the Markov Chain approach produces variates heta distributed according to P( heta|D) so moments are trivially obtained by summing of the ensemble of variates.

  11. Bayesian inference in geomagnetism

    NASA Technical Reports Server (NTRS)

    Backus, George E.

    1988-01-01

    The inverse problem in empirical geomagnetic modeling is investigated, with critical examination of recently published studies. Particular attention is given to the use of Bayesian inference (BI) to select the damping parameter lambda in the uniqueness portion of the inverse problem. The mathematical bases of BI and stochastic inversion are explored, with consideration of bound-softening problems and resolution in linear Gaussian BI. The problem of estimating the radial magnetic field B(r) at the earth core-mantle boundary from surface and satellite measurements is then analyzed in detail, with specific attention to the selection of lambda in the studies of Gubbins (1983) and Gubbins and Bloxham (1985). It is argued that the selection method is inappropriate and leads to lambda values much larger than those that would result if a reasonable bound on the heat flow at the CMB were assumed.

  12. Cobalamin deficiency, hyperhomocysteinemia, and dementia

    PubMed Central

    Werder, Steven F

    2010-01-01

    Introduction Although consensus guidelines recommend checking serum B12 in patients with dementia, clinicians are often faced with various questions: (1) Which patients should be tested? (2) What test should be ordered? (3) How are inferences made from such testing? (4) In addition to serum B12, should other tests be ordered? (5) Is B12 deficiency compatible with dementia of the Alzheimer’s type? (6) What is to be expected from treatment? (7) How is B12 deficiency treated? Methods On January 31st, 2009, a Medline search was performed revealing 1,627 citations related to cobalamin deficiency, hyperhomocysteinemia, and dementia. After limiting the search terms, all abstracts and/or articles and other references were categorized into six major groups (general, biochemistry, manifestations, associations and risks, evaluation, and treatment) and then reviewed in answering the above questions. Results The six major groups above are described in detail. Seventy-five key studies, series, and clinical trials were identified. Evidence-based suggestions for patient management were developed. Discussion Evidence is convincing that hyperhomocysteinemia, with or without hypovitaminosis B12, is a risk factor for dementia. In the absence of hyperhomocysteinemia, evidence is less convincing that hypovitaminosis B12 is a risk factor for dementia. B12 deficiency manifestations are variable and include abnormal psychiatric, neurological, gastrointestinal, and hematological findings. Radiological images of individuals with hyperhomocysteinemia frequently demonstrate leukoaraiosis. Assessing serum B12 and treatment of B12 deficiency is crucial for those cases in which pernicious anemia is suspected and may be useful for mild cognitive impairment and mild to moderate dementia. The serum B12 level is the standard initial test: 200 picograms per milliliter or less is low, and 201 to 350 picograms per milliliter is borderline low. Other tests may be indicated, including plasma

  13. Carnitine Deficiency and Pregnancy

    PubMed Central

    de Bruyn, Anouk; Jacquemyn, Yves; Kinget, Kristof; Eyskens, François

    2015-01-01

    We present two cases of carnitine deficiency in pregnancy. In our first case, systematic screening revealed L-carnitine deficiency in the first born of an asymptomatic mother. In the course of her second pregnancy, maternal carnitine levels showed a deficiency as well. In a second case, a mother known with carnitine deficiency under supplementation was followed throughout her pregnancy. Both pregnancies had an uneventful outcome. Because carnitine deficiency can have serious complications, supplementation with carnitine is advised. This supplementation should be continued throughout pregnancy according to plasma concentrations. PMID:26113999

  14. Carnitine Deficiency and Pregnancy.

    PubMed

    de Bruyn, Anouk; Jacquemyn, Yves; Kinget, Kristof; Eyskens, François

    2015-01-01

    We present two cases of carnitine deficiency in pregnancy. In our first case, systematic screening revealed L-carnitine deficiency in the first born of an asymptomatic mother. In the course of her second pregnancy, maternal carnitine levels showed a deficiency as well. In a second case, a mother known with carnitine deficiency under supplementation was followed throughout her pregnancy. Both pregnancies had an uneventful outcome. Because carnitine deficiency can have serious complications, supplementation with carnitine is advised. This supplementation should be continued throughout pregnancy according to plasma concentrations. PMID:26113999

  15. Bayes factors and multimodel inference

    USGS Publications Warehouse

    Link, W.A.; Barker, R.J.

    2009-01-01

    Multimodel inference has two main themes: model selection, and model averaging. Model averaging is a means of making inference conditional on a model set, rather than on a selected model, allowing formal recognition of the uncertainty associated with model choice. The Bayesian paradigm provides a natural framework for model averaging, and provides a context for evaluation of the commonly used AIC weights. We review Bayesian multimodel inference, noting the importance of Bayes factors. Noting the sensitivity of Bayes factors to the choice of priors on parameters, we define and propose nonpreferential priors as offering a reasonable standard for objective multimodel inference.

  16. Creatine deficiency syndromes.

    PubMed

    Schulze, Andreas

    2003-02-01

    Since the first description of a creatine deficiency syndrome, the guanidinoacetate methyltransferase (GAMT) deficiency, in 1994, the two further suspected creatine deficiency syndromes--the creatine transporter (CrT1) defect and the arginine:glycine amidinotransferase (AGAT) deficiency were disclosed. GAMT and AGAT deficiency have autosomal-recessive traits, whereas the CrT1 defect is a X-linked disorder. All patients reveal developmental delay/regression, mental retardation, and severe disturbance of their expressive and cognitive speech. The common feature of all creatine deficiency syndromes is the severe depletion of creatine/phosphocreatine in the brain. Only the GAMT deficiency is in addition characterized by accumulation of guanidinoacetic acid in brain and body fluids. Guanidinoacetic acid seems to be responsible for intractable seizures and the movement disorder, both exclusively found in GAMT deficiency. Treatment with oral creatine supplementation is in part successful in GAMT and AGAT deficiency, whereas in CrT1 defect it is not able to replenish creatine in the brain. Treatment of combined arginine restriction and ornithine substitution in GAMT deficiency is capable to decrease guanidinoacetic acid permanently and improves the clinical outcome. The lack of the creatine/phosphocreatine signal in the patient's brain by means of in vivo proton magnetic resonance spectroscopy is the common finding and the diagnostic clue in all three diseases. In AGAT deficiency guanidinoacetic acid is decreased, whereas creatine in blood was found to be normal. On the other hand the CrT1 defect is characterized by an increased concentration of creatine in blood and urine whereas guanidinoacetic acid concentration is normal. The increasing number of patients detected very recently suffering from a creatine deficiency syndrome and the unfavorable outcome highlights the need of further attempts in early recognition of affected individuals and in optimizing its treatment

  17. Causal Inference in Retrospective Studies.

    ERIC Educational Resources Information Center

    Holland, Paul W.; Rubin, Donald B.

    1988-01-01

    The problem of drawing causal inferences from retrospective case-controlled studies is considered. A model for causal inference in prospective studies is applied to retrospective studies. Limitations of case-controlled studies are formulated concerning relevant parameters that can be estimated in such studies. A coffee-drinking/myocardial…

  18. Improving Inferences from Multiple Methods.

    ERIC Educational Resources Information Center

    Shotland, R. Lance; Mark, Melvin M.

    1987-01-01

    Multiple evaluation methods (MEMs) can cause an inferential challenge, although there are strategies to strengthen inferences. Practical and theoretical issues involved in the use by social scientists of MEMs, three potential problems in drawing inferences from MEMs, and short- and long-term strategies for alleviating these problems are outlined.…

  19. Causal Inference and Developmental Psychology

    ERIC Educational Resources Information Center

    Foster, E. Michael

    2010-01-01

    Causal inference is of central importance to developmental psychology. Many key questions in the field revolve around improving the lives of children and their families. These include identifying risk factors that if manipulated in some way would foster child development. Such a task inherently involves causal inference: One wants to know whether…

  20. Learning to Observe "and" Infer

    ERIC Educational Resources Information Center

    Hanuscin, Deborah L.; Park Rogers, Meredith A.

    2008-01-01

    Researchers describe the need for students to have multiple opportunities and social interaction to learn about the differences between observation and inference and their role in developing scientific explanations (Harlen 2001; Simpson 2000). Helping children develop their skills of observation and inference in science while emphasizing the…

  1. INFERRING THE ECCENTRICITY DISTRIBUTION

    SciTech Connect

    Hogg, David W.; Bovy, Jo; Myers, Adam D.

    2010-12-20

    Standard maximum-likelihood estimators for binary-star and exoplanet eccentricities are biased high, in the sense that the estimated eccentricity tends to be larger than the true eccentricity. As with most non-trivial observables, a simple histogram of estimated eccentricities is not a good estimate of the true eccentricity distribution. Here, we develop and test a hierarchical probabilistic method for performing the relevant meta-analysis, that is, inferring the true eccentricity distribution, taking as input the likelihood functions for the individual star eccentricities, or samplings of the posterior probability distributions for the eccentricities (under a given, uninformative prior). The method is a simple implementation of a hierarchical Bayesian model; it can also be seen as a kind of heteroscedastic deconvolution. It can be applied to any quantity measured with finite precision-other orbital parameters, or indeed any astronomical measurements of any kind, including magnitudes, distances, or photometric redshifts-so long as the measurements have been communicated as a likelihood function or a posterior sampling.

  2. Inferring the Eccentricity Distribution

    NASA Astrophysics Data System (ADS)

    Hogg, David W.; Myers, Adam D.; Bovy, Jo

    2010-12-01

    Standard maximum-likelihood estimators for binary-star and exoplanet eccentricities are biased high, in the sense that the estimated eccentricity tends to be larger than the true eccentricity. As with most non-trivial observables, a simple histogram of estimated eccentricities is not a good estimate of the true eccentricity distribution. Here, we develop and test a hierarchical probabilistic method for performing the relevant meta-analysis, that is, inferring the true eccentricity distribution, taking as input the likelihood functions for the individual star eccentricities, or samplings of the posterior probability distributions for the eccentricities (under a given, uninformative prior). The method is a simple implementation of a hierarchical Bayesian model; it can also be seen as a kind of heteroscedastic deconvolution. It can be applied to any quantity measured with finite precision—other orbital parameters, or indeed any astronomical measurements of any kind, including magnitudes, distances, or photometric redshifts—so long as the measurements have been communicated as a likelihood function or a posterior sampling.

  3. Social Inference Through Technology

    NASA Astrophysics Data System (ADS)

    Oulasvirta, Antti

    Awareness cues are computer-mediated, real-time indicators of people’s undertakings, whereabouts, and intentions. Already in the mid-1970 s, UNIX users could use commands such as “finger” and “talk” to find out who was online and to chat. The small icons in instant messaging (IM) applications that indicate coconversants’ presence in the discussion space are the successors of “finger” output. Similar indicators can be found in online communities, media-sharing services, Internet relay chat (IRC), and location-based messaging applications. But presence and availability indicators are only the tip of the iceberg. Technological progress has enabled richer, more accurate, and more intimate indicators. For example, there are mobile services that allow friends to query and follow each other’s locations. Remote monitoring systems developed for health care allow relatives and doctors to assess the wellbeing of homebound patients (see, e.g., Tang and Venables 2000). But users also utilize cues that have not been deliberately designed for this purpose. For example, online gamers pay attention to other characters’ behavior to infer what the other players are like “in real life.” There is a common denominator underlying these examples: shared activities rely on the technology’s representation of the remote person. The other human being is not physically present but present only through a narrow technological channel.

  4. Inference from aging information.

    PubMed

    de Oliveira, Evaldo Araujo; Caticha, Nestor

    2010-06-01

    For many learning tasks the duration of the data collection can be greater than the time scale for changes of the underlying data distribution. The question we ask is how to include the information that data are aging. Ad hoc methods to achieve this include the use of validity windows that prevent the learning machine from making inferences based on old data. This introduces the problem of how to define the size of validity windows. In this brief, a new adaptive Bayesian inspired algorithm is presented for learning drifting concepts. It uses the analogy of validity windows in an adaptive Bayesian way to incorporate changes in the data distribution over time. We apply a theoretical approach based on information geometry to the classification problem and measure its performance in simulations. The uncertainty about the appropriate size of the memory windows is dealt with in a Bayesian manner by integrating over the distribution of the adaptive window size. Thus, the posterior distribution of the weights may develop algebraic tails. The learning algorithm results from tracking the mean and variance of the posterior distribution of the weights. It was found that the algebraic tails of this posterior distribution give the learning algorithm the ability to cope with an evolving environment by permitting the escape from local traps. PMID:20421181

  5. α1-Antitrypsin Deficiency.

    PubMed

    Hatipoğlu, Umur; Stoller, James K

    2016-09-01

    α1-Antitrypsin deficiency is an autosomal codominant condition that predisposes to emphysema and cirrhosis. The condition is common but grossly under-recognized. Identifying patients' α1-antitrypsin deficiency has important management implications (ie, smoking cessation, genetic and occupational counseling, and specific treatment with the infusion of pooled human plasma α1-antitrypsin). The weight of evidence suggests that augmentation therapy slows the progression of emphysema in individuals with severe α1-antitrypsin deficiency. PMID:27514595

  6. Ensemble Inference and Inferability of Gene Regulatory Networks

    PubMed Central

    Ud-Dean, S. M. Minhaz; Gunawan, Rudiyanto

    2014-01-01

    The inference of gene regulatory network (GRN) from gene expression data is an unsolved problem of great importance. This inference has been stated, though not proven, to be underdetermined implying that there could be many equivalent (indistinguishable) solutions. Motivated by this fundamental limitation, we have developed new framework and algorithm, called TRaCE, for the ensemble inference of GRNs. The ensemble corresponds to the inherent uncertainty associated with discriminating direct and indirect gene regulations from steady-state data of gene knock-out (KO) experiments. We applied TRaCE to analyze the inferability of random GRNs and the GRNs of E. coli and yeast from single- and double-gene KO experiments. The results showed that, with the exception of networks with very few edges, GRNs are typically not inferable even when the data are ideal (unbiased and noise-free). Finally, we compared the performance of TRaCE with top performing methods of DREAM4 in silico network inference challenge. PMID:25093509

  7. Iodine-deficiency disorders.

    PubMed

    Zimmermann, Michael B; Jooste, Pieter L; Pandav, Chandrakant S

    2008-10-01

    2 billion individuals worldwide have insufficient iodine intake, with those in south Asia and sub-Saharan Africa particularly affected. Iodine deficiency has many adverse effects on growth and development. These effects are due to inadequate production of thyroid hormone and are termed iodine-deficiency disorders. Iodine deficiency is the most common cause of preventable mental impairment worldwide. Assessment methods include urinary iodine concentration, goitre, newborn thyroid-stimulating hormone, and blood thyroglobulin. In nearly all countries, the best strategy to control iodine deficiency is iodisation of salt, which is one of the most cost-effective ways to contribute to economic and social development. When iodisation of salt is not possible, iodine supplements can be given to susceptible groups. Introduction of iodised salt to regions of chronic iodine-deficiency disorders might transiently increase the proportion of thyroid disorders, but overall the small risks of iodine excess are far outweighed by the substantial risks of iodine deficiency. International efforts to control iodine-deficiency disorders are slowing, and reaching the third of the worldwide population that remains deficient poses major challenges. PMID:18676011

  8. Vitamin deficiencies and excesses

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Vitamins are essential nutrients that must be supplied exogenously either as part of a well balanced diet or as supplements. Deficiency states are uncommon in developed countries except, perhaps, among some food insecure families. In contrast, deficiency states are quite common in many developing ...

  9. Testosterone deficiency myopathy.

    PubMed Central

    Orrell, R W; Woodrow, D F; Barrett, M C; Press, M; Dick, D J; Rowe, R C; Lane, R J

    1995-01-01

    Testosterone is recognized to have a positive effect on nitrogen balance and muscle development in hypogonadal men, but significantly myopathy secondary to testosterone deficiency has been reported only rarely. We describe a patient who presented with a myopathy associated with testosterone deficiency, and who demonstrated a significant functional and myometric response to treatment. PMID:7562829

  10. MENTAL DEFICIENCY. SECOND EDITION.

    ERIC Educational Resources Information Center

    HILLIARD, L.T.; KIRMAN, BRIAN H.

    REVISED TO INCLUDE LEGISLATIVE AND ADMINISTRATIVE PROCEDURES NEW IN BRITAIN SINCE THE 1957 EDITION, THE TEXT INCLUDES RECENT ADVANCES IN ETIOLOGY, PATHOLOGY, AND TREATMENT OF MENTAL DEFICIENCY. CONSIDERATION OF THE BACKGROUND OF MENTAL DEFICIENCY INCLUDES HISTORICAL AND LEGAL ASPECTS, THE SOCIAL BACKGROUND OF MENTAL DEFECT, PRENATAL CAUSES OF…

  11. Cerebral Folate Deficiency

    ERIC Educational Resources Information Center

    Gordon, Neil

    2009-01-01

    Cerebral folate deficiency (CFD) is associated with low levels of 5-methyltetrahydrofolate in the cerebrospinal fluid (CSF) with normal folate levels in the plasma and red blood cells. The onset of symptoms caused by the deficiency of folates in the brain is at around 4 to 6 months of age. This is followed by delayed development, with deceleration…

  12. Iron deficiency anemia

    MedlinePlus

    Anemia - iron deficiency ... iron from old red blood cells. Iron deficiency anemia develops when your body's iron stores run low. ... You may have no symptoms if the anemia is mild. Most of the time, ... slowly. Symptoms may include: Feeling weak or tired more often ...

  13. Factor X deficiency

    MedlinePlus

    Factor X (ten) deficiency is a disorder caused by a lack of a protein called factor X in the blood. It leads to problems with ... or are not functioning like they should. Factor X is one such coagulation factor. Factor X deficiency ...

  14. Iron induced nickel deficiency

    Technology Transfer Automated Retrieval System (TEKTRAN)

    It is increasingly apparent that economic loss due to nickel (Ni) deficiency likely occurs in horticultural and agronomic crops. While most soils contain sufficient Ni to meet crop requirements, situations of Ni deficiency can arise due to antagonistic interactions with other metals. This study asse...

  15. G6PD Deficiency

    MedlinePlus

    Glucose-6-phosphate dehydrogenase (G6PD) deficiency is a genetic disorder that is most common in males. About 1 in 10 African American males in the United States has it. G6PD deficiency mainly affects red blood cells, which carry oxygen ...

  16. Bayesian Inference: with ecological applications

    USGS Publications Warehouse

    Link, William A.; Barker, Richard J.

    2010-01-01

    This text provides a mathematically rigorous yet accessible and engaging introduction to Bayesian inference with relevant examples that will be of interest to biologists working in the fields of ecology, wildlife management and environmental studies as well as students in advanced undergraduate statistics.. This text opens the door to Bayesian inference, taking advantage of modern computational efficiencies and easily accessible software to evaluate complex hierarchical models.

  17. Active inference, communication and hermeneutics.

    PubMed

    Friston, Karl J; Frith, Christopher D

    2015-07-01

    Hermeneutics refers to interpretation and translation of text (typically ancient scriptures) but also applies to verbal and non-verbal communication. In a psychological setting it nicely frames the problem of inferring the intended content of a communication. In this paper, we offer a solution to the problem of neural hermeneutics based upon active inference. In active inference, action fulfils predictions about how we will behave (e.g., predicting we will speak). Crucially, these predictions can be used to predict both self and others--during speaking and listening respectively. Active inference mandates the suppression of prediction errors by updating an internal model that generates predictions--both at fast timescales (through perceptual inference) and slower timescales (through perceptual learning). If two agents adopt the same model, then--in principle--they can predict each other and minimise their mutual prediction errors. Heuristically, this ensures they are singing from the same hymn sheet. This paper builds upon recent work on active inference and communication to illustrate perceptual learning using simulated birdsongs. Our focus here is the neural hermeneutics implicit in learning, where communication facilitates long-term changes in generative models that are trying to predict each other. In other words, communication induces perceptual learning and enables others to (literally) change our minds and vice versa. PMID:25957007

  18. Causal inference and developmental psychology.

    PubMed

    Foster, E Michael

    2010-11-01

    Causal inference is of central importance to developmental psychology. Many key questions in the field revolve around improving the lives of children and their families. These include identifying risk factors that if manipulated in some way would foster child development. Such a task inherently involves causal inference: One wants to know whether the risk factor actually causes outcomes. Random assignment is not possible in many instances, and for that reason, psychologists must rely on observational studies. Such studies identify associations, and causal interpretation of such associations requires additional assumptions. Research in developmental psychology generally has relied on various forms of linear regression, but this methodology has limitations for causal inference. Fortunately, methodological developments in various fields are providing new tools for causal inference-tools that rely on more plausible assumptions. This article describes the limitations of regression for causal inference and describes how new tools might offer better causal inference. This discussion highlights the importance of properly identifying covariates to include (and exclude) from the analysis. This discussion considers the directed acyclic graph for use in accomplishing this task. With the proper covariates having been chosen, many of the available methods rely on the assumption of "ignorability." The article discusses the meaning of ignorability and considers alternatives to this assumption, such as instrumental variables estimation. Finally, the article considers the use of the tools discussed in the context of a specific research question, the effect of family structure on child development. PMID:20677855

  19. Active inference, communication and hermeneutics☆

    PubMed Central

    Friston, Karl J.; Frith, Christopher D.

    2015-01-01

    Hermeneutics refers to interpretation and translation of text (typically ancient scriptures) but also applies to verbal and non-verbal communication. In a psychological setting it nicely frames the problem of inferring the intended content of a communication. In this paper, we offer a solution to the problem of neural hermeneutics based upon active inference. In active inference, action fulfils predictions about how we will behave (e.g., predicting we will speak). Crucially, these predictions can be used to predict both self and others – during speaking and listening respectively. Active inference mandates the suppression of prediction errors by updating an internal model that generates predictions – both at fast timescales (through perceptual inference) and slower timescales (through perceptual learning). If two agents adopt the same model, then – in principle – they can predict each other and minimise their mutual prediction errors. Heuristically, this ensures they are singing from the same hymn sheet. This paper builds upon recent work on active inference and communication to illustrate perceptual learning using simulated birdsongs. Our focus here is the neural hermeneutics implicit in learning, where communication facilitates long-term changes in generative models that are trying to predict each other. In other words, communication induces perceptual learning and enables others to (literally) change our minds and vice versa. PMID:25957007

  20. Glucose-6-phosphate dehydrogenase deficiency

    MedlinePlus

    G-6-PD deficiency; Hemolytic anemia due to G6PD deficiency; Anemia - hemolytic due to G6PD deficiency ... Churchill Livingston; 2008:chap 45. Golan DER. Hemolytic anemias: red cell membrane and metabolic defects. In: Goldman ...

  1. Optimal inference with suboptimal models: Addiction and active Bayesian inference

    PubMed Central

    Schwartenbeck, Philipp; FitzGerald, Thomas H.B.; Mathys, Christoph; Dolan, Ray; Wurst, Friedrich; Kronbichler, Martin; Friston, Karl

    2015-01-01

    When casting behaviour as active (Bayesian) inference, optimal inference is defined with respect to an agent’s beliefs – based on its generative model of the world. This contrasts with normative accounts of choice behaviour, in which optimal actions are considered in relation to the true structure of the environment – as opposed to the agent’s beliefs about worldly states (or the task). This distinction shifts an understanding of suboptimal or pathological behaviour away from aberrant inference as such, to understanding the prior beliefs of a subject that cause them to behave less ‘optimally’ than our prior beliefs suggest they should behave. Put simply, suboptimal or pathological behaviour does not speak against understanding behaviour in terms of (Bayes optimal) inference, but rather calls for a more refined understanding of the subject’s generative model upon which their (optimal) Bayesian inference is based. Here, we discuss this fundamental distinction and its implications for understanding optimality, bounded rationality and pathological (choice) behaviour. We illustrate our argument using addictive choice behaviour in a recently described ‘limited offer’ task. Our simulations of pathological choices and addictive behaviour also generate some clear hypotheses, which we hope to pursue in ongoing empirical work. PMID:25561321

  2. Betaine deficiency in maize

    SciTech Connect

    Lerma, C. ); Rich, P.J.; Ju, G.C.; Yang, Wenju; Rhodes, D. ); Hanson, A.D. )

    1991-04-01

    Maize (Zea mays L.) is a betaine-accumulating species, but certain maize genotypes lack betaine almost completely; a single recessive gene has been implicated as the cause of this deficiency. This study was undertaken to determine whether betaine deficiency in diverse maize germplasm is conditioned by the same genetic locus, and to define the biochemical lesion(s) involved. Complementation tests indicated that all 13 deficient genotypes tested shared a common locus. One maize population (P77) was found to be segregating for betaine deficiency, and true breeding individuals were used to produce related lines with and without betaine. Leaf tissue of both betaine-positive and betaine-deficient lines readily converted supplied betaine aldehyde to betaine, but only the betaine-containing line was able to oxidize supplied choline to betaine. This locates the lesion in betaine-deficient plants at the choline {r arrow} betaine aldehyde step of betaine synthesis. Consistent with this location, betaine-deficient plants were shown to have no detectable endogenous pool of betaine aldehyde.

  3. Congenital limb deficiency disorders.

    PubMed

    Wilcox, William R; Coulter, Colleen P; Schmitz, Michael L

    2015-06-01

    Congenital limb deficiency disorders (LDDs) are birth defects characterized by the aplasia or hypoplasia of bones of the limbs. Limb deficiencies are classified as transverse, those due to intrauterine disruptions of previously normal limbs, or longitudinal, those that are isolated or associated with certain syndromes as well as chromosomal anomalies. Consultation with a medical geneticist is advisable. Long-term care should occur in a specialized limb deficiency center with expertise in orthopedics, prosthetics, and occupational and physical therapy and provide emotional support and contact with other families. With appropriate care, most children with LDDs can lead productive lives. PMID:26042905

  4. Iron deficiency anemia

    PubMed Central

    Naigamwalla, Dinaz Z.; Webb, Jinelle A.; Giger, Urs

    2012-01-01

    Iron is essential to virtually all living organisms and is integral to multiple metabolic functions. The most important function is oxygen transport in hemoglobin. Iron deficiency anemia in dogs and cats is usually caused by chronic blood loss and can be discovered incidentally as animals may have adapted to the anemia. Severe iron deficiency is characterized by a microcytic, hypochromic, potentially severe anemia with a variable regenerative response. Iron metabolism and homeostasis will be reviewed, followed by a discussion of diagnostic testing and therapeutic recommendations for dogs and cats with iron deficiency anemia. PMID:22942439

  5. Thiamine deficiency and delirium.

    PubMed

    Osiezagha, Kenneth; Ali, Shahid; Freeman, C; Barker, Narviar C; Jabeen, Shagufta; Maitra, Sarbani; Olagbemiro, Yetunde; Richie, William; Bailey, Rahn K

    2013-04-01

    Thiamine is an essential vitamin that plays an important role in cellular production of energy from ingested food and enhances normal neuronal actives. Deficiency of this vitamin leads to a very serious clinical condition known as delirium. Studies performed in the United States and other parts of the world have established the link between thiamine deficiency and delirium. This literature review examines the physiology, pathophysiology, predisposing factors, clinical manifestations (e.g., Wernicke's encephalopathy, Wernicke-Korsakoff syndrome, structural and functional brain injuries) and diagnosis of thiamine deficiency and delirium. Current treatment practices are also discussed that may improve patient outcome, which ultimately may result in a reduction in healthcare costs. PMID:23696956

  6. Statistical inference and string theory

    NASA Astrophysics Data System (ADS)

    Heckman, Jonathan J.

    2015-09-01

    In this paper, we expose some surprising connections between string theory and statistical inference. We consider a large collective of agents sweeping out a family of nearby statistical models for an M-dimensional manifold of statistical fitting parameters. When the agents making nearby inferences align along a d-dimensional grid, we find that the pooled probability that the collective reaches a correct inference is the partition function of a nonlinear sigma model in d dimensions. Stability under perturbations to the original inference scheme requires the agents of the collective to distribute along two dimensions. Conformal invariance of the sigma model corresponds to the condition of a stable inference scheme, directly leading to the Einstein field equations for classical gravity. By summing over all possible arrangements of the agents in the collective, we reach a string theory. We also use this perspective to quantify how much an observer can hope to learn about the internal geometry of a superstring compactification. Finally, we present some brief speculative remarks on applications to the AdS/CFT correspondence and Lorentzian signature space-times.

  7. Familial lipoprotein lipase deficiency

    MedlinePlus

    ... and white-colored blood vessels in the retinas Pancreatitis that keeps returning Yellowing of the eyes and ... discuss your diet needs with a registered dietitian. Pancreatitis that is related to lipoprotein lipase deficiency responds ...

  8. Growth hormone deficiency - children

    MedlinePlus

    ... the same age. The child will have normal intelligence in most cases. In older children, puberty may ... hormones cause the body to make. Tests can measure these growth factors. Accurate growth hormone deficiency testing ...

  9. Vitamin D Deficiency

    MedlinePlus

    ... deficiency can lead to a loss of bone density (size and strength), broken bones (fractures), muscle weakness, ... get too much calcium in their blood or urine. Careful monitoring of blood vitamin D levels will ...

  10. Factor V deficiency

    MedlinePlus

    ... as many as 20 different proteins in blood plasma. These proteins are called blood coagulation factors. Factor ... You will be given fresh blood plasma or fresh frozen plasma infusions ... These treatments will correct the deficiency temporarily.

  11. Folate-deficiency anemia

    MedlinePlus

    Folate-deficiency anemia is a decrease in red blood cells (anemia) due to a lack of folate. Folate is a type ... B vitamin. It is also called folic acid. Anemia is a condition in which the body does ...

  12. Clinical significance of complement deficiencies.

    PubMed

    Pettigrew, H David; Teuber, Suzanne S; Gershwin, M Eric

    2009-09-01

    The complement system is composed of more than 30 serum and membrane-bound proteins, all of which are needed for normal function of complement in innate and adaptive immunity. Historically, deficiencies within the complement system have been suspected when young children have had recurrent and difficult-to-control infections. As our understanding of the complement system has increased, many other diseases have been attributed to deficiencies within the complement system. Generally, complement deficiencies within the classical pathway lead to increased susceptibility to encapsulated bacterial infections as well as a syndrome resembling systemic lupus erythematosus. Complement deficiencies within the mannose-binding lectin pathway generally lead to increased bacterial infections, and deficiencies within the alternative pathway usually lead to an increased frequency of Neisseria infections. However, factor H deficiency can lead to membranoproliferative glomerulonephritis and hemolytic uremic syndrome. Finally, deficiencies within the terminal complement pathway lead to an increased incidence of Neisseria infections. Two other notable complement-associated deficiencies are complement receptor 3 and 4 deficiency, which result from a deficiency of CD18, a disease known as leukocyte adhesion deficiency type 1, and CD59 deficiency, which causes paroxysmal nocturnal hemoglobinuria. Most inherited deficiencies of the complement system are autosomal recessive, but properidin deficiency is X-linked recessive, deficiency of C1 inhibitor is autosomal dominant, and mannose-binding lectin and factor I deficiencies are autosomal co-dominant. The diversity of clinical manifestations of complement deficiencies reflects the complexity of the complement system. PMID:19758139

  13. Thermodynamics of cellular statistical inference

    NASA Astrophysics Data System (ADS)

    Lang, Alex; Fisher, Charles; Mehta, Pankaj

    2014-03-01

    Successful organisms must be capable of accurately sensing the surrounding environment in order to locate nutrients and evade toxins or predators. However, single cell organisms face a multitude of limitations on their accuracy of sensing. Berg and Purcell first examined the canonical example of statistical limitations to cellular learning of a diffusing chemical and established a fundamental limit to statistical accuracy. Recent work has shown that the Berg and Purcell learning limit can be exceeded using Maximum Likelihood Estimation. Here, we recast the cellular sensing problem as a statistical inference problem and discuss the relationship between the efficiency of an estimator and its thermodynamic properties. We explicitly model a single non-equilibrium receptor and examine the constraints on statistical inference imposed by noisy biochemical networks. Our work shows that cells must balance sample number, specificity, and energy consumption when performing statistical inference. These tradeoffs place significant constraints on the practical implementation of statistical estimators in a cell.

  14. Causal inference from observational data.

    PubMed

    Listl, Stefan; Jürges, Hendrik; Watt, Richard G

    2016-10-01

    Randomized controlled trials have long been considered the 'gold standard' for causal inference in clinical research. In the absence of randomized experiments, identification of reliable intervention points to improve oral health is often perceived as a challenge. But other fields of science, such as social science, have always been challenged by ethical constraints to conducting randomized controlled trials. Methods have been established to make causal inference using observational data, and these methods are becoming increasingly relevant in clinical medicine, health policy and public health research. This study provides an overview of state-of-the-art methods specifically designed for causal inference in observational data, including difference-in-differences (DiD) analyses, instrumental variables (IV), regression discontinuity designs (RDD) and fixed-effects panel data analysis. The described methods may be particularly useful in dental research, not least because of the increasing availability of routinely collected administrative data and electronic health records ('big data'). PMID:27111146

  15. We infer light in space.

    PubMed

    Schirillo, James A

    2013-10-01

    In studies of lightness and color constancy, the terms lightness and brightness refer to the qualia corresponding to perceived surface reflectance and perceived luminance, respectively. However, what has rarely been considered is the fact that the volume of space containing surfaces appears neither empty, void, nor black, but filled with light. Helmholtz (1866/1962) came closest to describing this phenomenon when discussing inferred illumination, but previous theoretical treatments have fallen short by restricting their considerations to the surfaces of objects. The present work is among the first to explore how we infer the light present in empty space. It concludes with several research examples supporting the theory that humans can infer the differential levels and chromaticities of illumination in three-dimensional space. PMID:23435628

  16. Eight challenges in phylodynamic inference

    PubMed Central

    Frost, Simon D.W.; Pybus, Oliver G.; Gog, Julia R.; Viboud, Cecile; Bonhoeffer, Sebastian; Bedford, Trevor

    2015-01-01

    The field of phylodynamics, which attempts to enhance our understanding of infectious disease dynamics using pathogen phylogenies, has made great strides in the past decade. Basic epidemiological and evolutionary models are now well characterized with inferential frameworks in place. However, significant challenges remain in extending phylodynamic inference to more complex systems. These challenges include accounting for evolutionary complexities such as changing mutation rates, selection, reassortment, and recombination, as well as epidemiological complexities such as stochastic population dynamics, host population structure, and different patterns at the within-host and between-host scales. An additional challenge exists in making efficient inferences from an ever increasing corpus of sequence data. PMID:25843391

  17. Inferring biotic interactions from proxies.

    PubMed

    Morales-Castilla, Ignacio; Matias, Miguel G; Gravel, Dominique; Araújo, Miguel B

    2015-06-01

    Inferring biotic interactions from functional, phylogenetic and geographical proxies remains one great challenge in ecology. We propose a conceptual framework to infer the backbone of biotic interaction networks within regional species pools. First, interacting groups are identified to order links and remove forbidden interactions between species. Second, additional links are removed by examination of the geographical context in which species co-occur. Third, hypotheses are proposed to establish interaction probabilities between species. We illustrate the framework using published food-webs in terrestrial and marine systems. We conclude that preliminary descriptions of the web of life can be made by careful integration of data with theory. PMID:25922148

  18. VERMILION-DEFICIENCY.

    PubMed

    Bridges, C B

    1919-07-20

    In May, 1916, a culture of Drosophila melanogaster showed that a new sex-linked lethal had arisen. The linkage relations indicated that the position of the lethal was in the neighborhood of the sex-linked recessive "vermilion," whose locus in the X chromosome is at 33.0. When females heterozygous for the lethal were outcrossed to vermilion males, all the daughters that received the lethal-bearing chromosome showed vermilion eye-color, though, from the pedigree, vermilion was known to be absent from the ancestry of the mother. The lethal action and the unexpected appearance of vermilion both suggested that this was another instance of the phenomenon called "deficiency;" that is, the loss or "inactivation" of the genes of a section of the X chromosome. The lethal action would then be due to the deficient region including one or more genes necessary for the life of the individual. The appearance of vermilion in females carrying only one vermilion gene would be explainable on the ground that the deficient-bearing females are virtually haploid for the region including the vermilion locus. Linkage tests showed that the amount of crossing over in the neighborhood of the deficiency was cut down by about five units. Part of this may be attributed to the actual length of the "deficient" region, within which it is probable that no crossing over occurs, and part (probably most) to an alteration in the synaptic relations in the regions immediately adjacent. In more remote regions there was no disturbance or perhaps a slight rise in the frequency of crossing over. Both the local fall and the possible rise in more distant regions would seem to argue that a "pucker" at synapsis had been caused by an actual shortening of the deficient chromosome. That the deficient region extends to the left of the locus of vermilion was indicated by a test in which it was observed that the presence of an extra piece of chromosome including the loci for vermilion and sable ("vermilion

  19. Iron deficiency in Europe.

    PubMed

    Hercberg, S; Preziosi, P; Galan, P

    2001-04-01

    In Europe, iron deficiency is considered to be one of the main nutritional deficiency disorders affecting large fractions of the population, particularly such physiological groups as children, menstruating women and pregnant women. Some factors such as type of contraception in women, blood donation or minor pathological blood loss (haemorrhoids, gynaecological bleeding...) considerably increase the difficulty of covering iron needs. Moreover, women, especially adolescents consuming low-energy diets, vegetarians and vegans are at high risk of iron deficiency. Although there is no evidence that an absence of iron stores has any adverse consequences, it does indicate that iron nutrition is borderline, since any further reduction in body iron is associated with a decrease in the level of functional compounds such as haemoglobin. The prevalence of iron-deficient anaemia has slightly decreased in infants and menstruating women. Some positive factors may have contributed to reducing the prevalence of iron-deficiency anaemia in some groups of population: the use of iron-fortified formulas and iron-fortified cereals; the use of oral contraceptives and increased enrichment of iron in several countries; and the use of iron supplements during pregnancy in some European countries. It is possible to prevent and control iron deficiency by counseling individuals and families about sound iron nutrition during infancy and beyond, and about iron supplementation during pregnancy, by screening persons on the basis of their risk for iron deficiency, and by treating and following up persons with presumptive iron deficiency. This may help to reduce manifestations of iron deficiency and thus improve public health. Evidence linking iron status with risk of cardiovascular disease or cancer is unconvincing and does not justify changes in food fortification or medical practice, particularly because the benefits of assuring adequate iron intake during growth and development are well established

  20. Science Shorts: Observation versus Inference

    ERIC Educational Resources Information Center

    Leager, Craig R.

    2008-01-01

    When you observe something, how do you know for sure what you are seeing, feeling, smelling, or hearing? Asking students to think critically about their encounters with the natural world will help to strengthen their understanding and application of the science-process skills of observation and inference. In the following lesson, students make…

  1. Sample Size and Correlational Inference

    ERIC Educational Resources Information Center

    Anderson, Richard B.; Doherty, Michael E.; Friedrich, Jeff C.

    2008-01-01

    In 4 studies, the authors examined the hypothesis that the structure of the informational environment makes small samples more informative than large ones for drawing inferences about population correlations. The specific purpose of the studies was to test predictions arising from the signal detection simulations of R. B. Anderson, M. E. Doherty,…

  2. Word Learning as Bayesian Inference

    ERIC Educational Resources Information Center

    Xu, Fei; Tenenbaum, Joshua B.

    2007-01-01

    The authors present a Bayesian framework for understanding how adults and children learn the meanings of words. The theory explains how learners can generalize meaningfully from just one or a few positive examples of a novel word's referents, by making rational inductive inferences that integrate prior knowledge about plausible word meanings with…

  3. The mechanisms of temporal inference

    NASA Technical Reports Server (NTRS)

    Fox, B. R.; Green, S. R.

    1987-01-01

    The properties of a temporal language are determined by its constituent elements: the temporal objects which it can represent, the attributes of those objects, the relationships between them, the axioms which define the default relationships, and the rules which define the statements that can be formulated. The methods of inference which can be applied to a temporal language are derived in part from a small number of axioms which define the meaning of equality and order and how those relationships can be propagated. More complex inferences involve detailed analysis of the stated relationships. Perhaps the most challenging area of temporal inference is reasoning over disjunctive temporal constraints. Simple forms of disjunction do not sufficiently increase the expressive power of a language while unrestricted use of disjunction makes the analysis NP-hard. In many cases a set of disjunctive constraints can be converted to disjunctive normal form and familiar methods of inference can be applied to the conjunctive sub-expressions. This process itself is NP-hard but it is made more tractable by careful expansion of a tree-structured search space.

  4. Perceptual Inference and Autistic Traits

    ERIC Educational Resources Information Center

    Skewes, Joshua C; Jegindø, Else-Marie; Gebauer, Line

    2015-01-01

    Autistic people are better at perceiving details. Major theories explain this in terms of bottom-up sensory mechanisms or in terms of top-down cognitive biases. Recently, it has become possible to link these theories within a common framework. This framework assumes that perception is implicit neural inference, combining sensory evidence with…

  5. Improving Explanatory Inferences from Assessments

    ERIC Educational Resources Information Center

    Diakow, Ronli Phyllis

    2013-01-01

    This dissertation comprises three papers that propose, discuss, and illustrate models to make improved inferences about research questions regarding student achievement in education. Addressing the types of questions common in educational research today requires three different "extensions" to traditional educational assessment: (1)…

  6. Iron deficiency anaemia.

    PubMed

    Lopez, Anthony; Cacoub, Patrice; Macdougall, Iain C; Peyrin-Biroulet, Laurent

    2016-02-27

    Anaemia affects roughly a third of the world's population; half the cases are due to iron deficiency. It is a major and global public health problem that affects maternal and child mortality, physical performance, and referral to health-care professionals. Children aged 0-5 years, women of childbearing age, and pregnant women are particularly at risk. Several chronic diseases are frequently associated with iron deficiency anaemia--notably chronic kidney disease, chronic heart failure, cancer, and inflammatory bowel disease. Measurement of serum ferritin, transferrin saturation, serum soluble transferrin receptors, and the serum soluble transferrin receptors-ferritin index are more accurate than classic red cell indices in the diagnosis of iron deficiency anaemia. In addition to the search for and treatment of the cause of iron deficiency, treatment strategies encompass prevention, including food fortification and iron supplementation. Oral iron is usually recommended as first-line therapy, but the most recent intravenous iron formulations, which have been available for nearly a decade, seem to replenish iron stores safely and effectively. Hepcidin has a key role in iron homoeostasis and could be a future diagnostic and therapeutic target. In this Seminar, we discuss the clinical presentation, epidemiology, pathophysiology, diagnosis, and acute management of iron deficiency anaemia, and outstanding research questions for treatment. PMID:26314490

  7. Antepartum ornithine transcarbamylase deficiency.

    PubMed

    Nakajima, Hitoshi; Sasaki, Yosuke; Maeda, Tadashi; Takeda, Masako; Hara, Noriko; Nakanishi, Kazushige; Urita, Yoshihisa; Hattori, Risa; Miura, Ken; Taniguchi, Tomoko

    2014-01-01

    Ornithine transcarbamylase deficiency (OTCD) is the most common type urea cycle enzyme deficiencies. This syndrome results from a deficiency of the mitochondrial enzyme ornithine transcarbamylase, which catalyzes the conversion of ornithine and carbamoyl phosphate to citrullin. Our case was a 28-year-old female diagnosed with OTCD following neurocognitive deficit during her first pregnancy. Although hyperammonemia was suspected as the cause of the patient's mental changes, there was no evidence of chronic liver disease. Plasma amino acid and urine organic acid analysis revealed OTCD. After combined modality treatment with arginine, sodium benzoate and hemodialysis, the patient's plasma ammonia level stabilized and her mental status returned to normal. At last she recovered without any damage left. PMID:25759629

  8. Transient neonatal zinc deficiency.

    PubMed

    Krieger, I; Alpern, B E; Cunnane, S C

    1986-06-01

    We report an infant who developed clinical manifestations of zinc deficiency during the first month of life although the diet was adequate for zinc and no other causes could be ascertained. The diagnosis was confirmed by low plasma-zinc concentrations and a positive response to zinc treatment. The fatty acid profile of plasma phospholipids was typical of zinc deficiency (ie, arachidonic acid was markedly decreased). The transient nature of this disorder was evident when no relapse occurred after cessation of zinc therapy and plasma-zinc and arachidonic acid concentrations remained normal. Several explanations for the development of transient neonatal zinc deficiency are offered. The observation demonstrates that occasional infants may have requirements for zinc that are beyond the intakes of the conventional RDA. PMID:3717070

  9. Natural killer cell deficiency

    PubMed Central

    Orange, Jordan S.

    2013-01-01

    Natural killer (NK) cells are part of the innate immune defense against infection and cancer, and are especially useful in combating certain viral pathogens. The utility of NK cells in human health has been underscored by a growing number of individuals who are deficient in NK cells and/or their functions. This can be in the context of a broader genetically-defined congenital immunodeficiency of which there are over forty presently known to impair NK cells. The abnormality of NK cells, however, in certain cases represents the majority immunological defect. In aggregate, these conditions are termed NK cell deficiency. Recent advances have added clarity to this diagnosis and identified defects in three different genes that can cause NK cell deficiency as well as some of the underlying biology. Appropriate consideration of these diagnoses and patients raises the potential for rational therapeutic options and further innovation. PMID:23993353

  10. Thiamine Deficiency and Delirium

    PubMed Central

    Ali, Shahid; Freeman, C.; Barker, Narviar C.; Jabeen, Shagufta; Maitra, Sarbani; Olagbemiro, Yetunde; Richie, William; Bailey, Rahn K.

    2013-01-01

    Thiamine is an essential vitamin that plays an important role in cellular production of energy from ingested food and enhances normal neuronal actives. Deficiency of this vitamin leads to a very serious clinical condition known as delirium. Studies performed in the United States and other parts of the world have established the link between thiamine deficiency and delirium. This literature review examines the physiology, pathophysiology, predisposing factors, clinical manifestations (e.g., Wernicke’s encephalopathy, Wernicke-Korsakoff syndrome, structural and functional brain injuries) and diagnosis of thiamine deficiency and delirium. Current treatment practices are also discussed that may improve patient outcome, which ultimately may result in a reduction in healthcare costs. PMID:23696956

  11. A Deficiency of Credulousness.

    ERIC Educational Resources Information Center

    Brewer, Richard

    1992-01-01

    Asks the question: how does society assist citizens to stop deluding themselves with ESP, UFOs, astrology, polygraphy, water dowsing, channeling, and all manner of New Age gimcrackery? Supplies an answer: educators should emphasize instruction in probability models and scientific inference, while imparting an appropriate, scientific skepticism to…

  12. Bayesian Inference on Proportional Elections

    PubMed Central

    Brunello, Gabriel Hideki Vatanabe; Nakano, Eduardo Yoshio

    2015-01-01

    Polls for majoritarian voting systems usually show estimates of the percentage of votes for each candidate. However, proportional vote systems do not necessarily guarantee the candidate with the most percentage of votes will be elected. Thus, traditional methods used in majoritarian elections cannot be applied on proportional elections. In this context, the purpose of this paper was to perform a Bayesian inference on proportional elections considering the Brazilian system of seats distribution. More specifically, a methodology to answer the probability that a given party will have representation on the chamber of deputies was developed. Inferences were made on a Bayesian scenario using the Monte Carlo simulation technique, and the developed methodology was applied on data from the Brazilian elections for Members of the Legislative Assembly and Federal Chamber of Deputies in 2010. A performance rate was also presented to evaluate the efficiency of the methodology. Calculations and simulations were carried out using the free R statistical software. PMID:25786259

  13. Bayesian inference on proportional elections.

    PubMed

    Brunello, Gabriel Hideki Vatanabe; Nakano, Eduardo Yoshio

    2015-01-01

    Polls for majoritarian voting systems usually show estimates of the percentage of votes for each candidate. However, proportional vote systems do not necessarily guarantee the candidate with the most percentage of votes will be elected. Thus, traditional methods used in majoritarian elections cannot be applied on proportional elections. In this context, the purpose of this paper was to perform a Bayesian inference on proportional elections considering the Brazilian system of seats distribution. More specifically, a methodology to answer the probability that a given party will have representation on the chamber of deputies was developed. Inferences were made on a Bayesian scenario using the Monte Carlo simulation technique, and the developed methodology was applied on data from the Brazilian elections for Members of the Legislative Assembly and Federal Chamber of Deputies in 2010. A performance rate was also presented to evaluate the efficiency of the methodology. Calculations and simulations were carried out using the free R statistical software. PMID:25786259

  14. System Support for Forensic Inference

    NASA Astrophysics Data System (ADS)

    Gehani, Ashish; Kirchner, Florent; Shankar, Natarajan

    Digital evidence is playing an increasingly important role in prosecuting crimes. The reasons are manifold: financially lucrative targets are now connected online, systems are so complex that vulnerabilities abound and strong digital identities are being adopted, making audit trails more useful. If the discoveries of forensic analysts are to hold up to scrutiny in court, they must meet the standard for scientific evidence. Software systems are currently developed without consideration of this fact. This paper argues for the development of a formal framework for constructing “digital artifacts” that can serve as proxies for physical evidence; a system so imbued would facilitate sound digital forensic inference. A case study involving a filesystem augmentation that provides transparent support for forensic inference is described.

  15. Statistical learning and selective inference

    PubMed Central

    Taylor, Jonathan; Tibshirani, Robert J.

    2015-01-01

    We describe the problem of “selective inference.” This addresses the following challenge: Having mined a set of data to find potential associations, how do we properly assess the strength of these associations? The fact that we have “cherry-picked”—searched for the strongest associations—means that we must set a higher bar for declaring significant the associations that we see. This challenge becomes more important in the era of big data and complex statistical modeling. The cherry tree (dataset) can be very large and the tools for cherry picking (statistical learning methods) are now very sophisticated. We describe some recent new developments in selective inference and illustrate their use in forward stepwise regression, the lasso, and principal components analysis. PMID:26100887

  16. Network Plasticity as Bayesian Inference

    PubMed Central

    Legenstein, Robert; Maass, Wolfgang

    2015-01-01

    General results from statistical learning theory suggest to understand not only brain computations, but also brain plasticity as probabilistic inference. But a model for that has been missing. We propose that inherently stochastic features of synaptic plasticity and spine motility enable cortical networks of neurons to carry out probabilistic inference by sampling from a posterior distribution of network configurations. This model provides a viable alternative to existing models that propose convergence of parameters to maximum likelihood values. It explains how priors on weight distributions and connection probabilities can be merged optimally with learned experience, how cortical networks can generalize learned information so well to novel experiences, and how they can compensate continuously for unforeseen disturbances of the network. The resulting new theory of network plasticity explains from a functional perspective a number of experimental data on stochastic aspects of synaptic plasticity that previously appeared to be quite puzzling. PMID:26545099

  17. Causal inference based on counterfactuals

    PubMed Central

    Höfler, M

    2005-01-01

    Background The counterfactual or potential outcome model has become increasingly standard for causal inference in epidemiological and medical studies. Discussion This paper provides an overview on the counterfactual and related approaches. A variety of conceptual as well as practical issues when estimating causal effects are reviewed. These include causal interactions, imperfect experiments, adjustment for confounding, time-varying exposures, competing risks and the probability of causation. It is argued that the counterfactual model of causal effects captures the main aspects of causality in health sciences and relates to many statistical procedures. Summary Counterfactuals are the basis of causal inference in medicine and epidemiology. Nevertheless, the estimation of counterfactual differences pose several difficulties, primarily in observational studies. These problems, however, reflect fundamental barriers only when learning from observations, and this does not invalidate the counterfactual concept. PMID:16159397

  18. Color vision deficiencies

    NASA Astrophysics Data System (ADS)

    Vannorren, D.

    1982-04-01

    Congenital and acquired color vision defects are described in the context of physiological data. Light sources, photometry, color systems and test methods are described. A list of medicines is also presented. The practical social consequences of color vision deficiencies are discussed.

  19. Arginase-1 deficiency.

    PubMed

    Sin, Yuan Yan; Baron, Garrett; Schulze, Andreas; Funk, Colin D

    2015-12-01

    Arginase-1 (ARG1) deficiency is a rare autosomal recessive disorder that affects the liver-based urea cycle, leading to impaired ureagenesis. This genetic disorder is caused by 40+ mutations found fairly uniformly spread throughout the ARG1 gene, resulting in partial or complete loss of enzyme function, which catalyzes the hydrolysis of arginine to ornithine and urea. ARG1-deficient patients exhibit hyperargininemia with spastic paraparesis, progressive neurological and intellectual impairment, persistent growth retardation, and infrequent episodes of hyperammonemia, a clinical pattern that differs strikingly from other urea cycle disorders. This review briefly highlights the current understanding of the etiology and pathophysiology of ARG1 deficiency derived from clinical case reports and therapeutic strategies stretching over several decades and reports on several exciting new developments regarding the pathophysiology of the disorder using ARG1 global and inducible knockout mouse models. Gene transfer studies in these mice are revealing potential therapeutic options that can be exploited in the future. However, caution is advised in extrapolating results since the lethal disease phenotype in mice is much more severe than in humans indicating that the mouse models may not precisely recapitulate human disease etiology. Finally, some of the functions and implications of ARG1 in non-urea cycle activities are considered. Lingering questions and future areas to be addressed relating to the clinical manifestations of ARG1 deficiency in liver and brain are also presented. Hopefully, this review will spark invigorated research efforts that lead to treatments with better clinical outcomes. PMID:26467175

  20. Self-enforcing Private Inference Control

    NASA Astrophysics Data System (ADS)

    Yang, Yanjiang; Li, Yingjiu; Weng, Jian; Zhou, Jianying; Bao, Feng

    Private inference control enables simultaneous enforcement of inference control and protection of users' query privacy. Private inference control is a useful tool for database applications, especially when users are increasingly concerned about individual privacy nowadays. However, protection of query privacy on top of inference control is a double-edged sword: without letting the database server know the content of user queries, users can easily launch DoS attacks. To assuage DoS attacks in private inference control, we propose the concept of self-enforcing private inference control, whose intuition is to force users to only make inference-free queries by enforcing inference control themselves; otherwise, penalty will inflict upon the violating users.

  1. Genetics Home Reference: biotinidase deficiency

    MedlinePlus

    ... Aydin HI, Sennaroğlu L, Belgin E, Jensen K, Wolf B. Hearing loss in biotinidase deficiency: genotype-phenotype ... corrected to Aydin, Halil Ibrahim]. Citation on PubMed Wolf B. Biotinidase deficiency: "if you have to have ...

  2. Factor XII (Hageman factor) deficiency

    MedlinePlus

    ... takes longer than normal to clot in a test tube. Factor XII deficiency is a rare inherited disorder. Symptoms There are usually no symptoms. Exams and Tests Factor XII deficiency is most often found when ...

  3. Genetics Home Reference: pseudocholinesterase deficiency

    MedlinePlus

    ... deficiency is a condition that results in increased sensitivity to certain muscle relaxant drugs used during general ... People with pseudocholinesterase deficiency may also have increased sensitivity to certain other drugs, including the local anesthetic ...

  4. Transient partial growth hormone deficiency due to zinc deficiency.

    PubMed

    Nishi, Y; Hatano, S; Aihara, K; Fujie, A; Kihara, M

    1989-04-01

    We present here a 13-year-old boy with partial growth hormone deficiency due to chronic mild zinc deficiency. When zinc administration was started, his growth rate, growth hormone levels, and plasma zinc concentrations increased significantly. His poor dietary intake resulted in chronic mild zinc deficiency, which in turn could be the cause of a further loss of appetite and growth retardation. There was also a possibility of renal zinc wasting which may have contributed to zinc deficiency. Zinc deficiency should be carefully ruled out in patients with growth retardation. PMID:2708733

  5. Glucose-6-phosphate dehydrogenase deficiency

    MedlinePlus

    G6PD deficiency; Hemolytic anemia due to G6PD deficiency; Anemia - hemolytic due to G6PD deficiency ... Gallagher PG. Hemolytic anemias. In: Goldman L, Schafer AI, eds. Goldman's Cecil Medicine . 25th ed. Philadelphia, PA: Elsevier Saunders; 2016:chap 161. Janz ...

  6. Growth and cesium uptake responses of Phytolacca americana Linn. and Amaranthus cruentus L. grown on cesium contaminated soil to elevated CO2 or inoculation with a plant growth promoting rhizobacterium Burkholderia sp. D54, or in combination.

    PubMed

    Tang, Shirong; Liao, Shangqiang; Guo, Junkang; Song, Zhengguo; Wang, Ruigang; Zhou, Xiaomin

    2011-12-30

    Growth and cesium uptake responses of plants to elevated CO(2) and microbial inoculation, alone or in combination, can be explored for clean-up of contaminated soils, and this induced phytoextraction may be better than the natural process. The present study used open-top chambers to investigate combined effects of Burkholderia sp. D54 inoculation and elevated CO(2) (860 μL L(-1)) on growth and Cs uptake by Phytolacca americana and Amaranthus cruentus grown on soil spiked with various levels of Cs (0-1000 mg kg(-1)). Elevated CO(2) and bacterial inoculation, alone or in combination, significantly increased biomass production with increased magnitude, ranging from 22% to 139% for P. americana, and 14% to 254% for A. cruentus. Total tissue Cs in both plants was significantly greater for bacterial inoculation treatment singly, and combined treatments of bacterial inoculation and elevated CO(2) than for the control treatment in most cases. Regardless of CO(2) concentrations and bacterial inoculation, A. cruentus had higher tissue Cs concentration, Cs transfer factors and concentration ratios than P. americana, but they had slightly different contents of antioxidant enzymes. It is concluded that combined effects of elevated CO(2) and microbial inoculation with regard to plant ability to grow and remove radionuclides from soil can be explored for CO(2)- and microbe-assisted phytoextraction technology. PMID:22074893

  7. Molybdenum cofactor deficiency.

    PubMed

    Atwal, Paldeep S; Scaglia, Fernando

    2016-01-01

    Molybdenum cofactor deficiency (MoCD) is a severe autosomal recessive inborn error of metabolism first described in 1978. It is characterized by a neonatal presentation of intractable seizures, feeding difficulties, severe developmental delay, microcephaly with brain atrophy and coarse facial features. MoCD results in deficiency of the molybdenum cofactor dependent enzymes sulfite oxidase, xanthine dehydrogenase, aldehyde oxidase and mitochondrial amidoxime reducing component. The resultant accumulation of sulfite, taurine, S-sulfocysteine and thiosulfate contributes to the severe neurological impairment. Recently, initial evidence has demonstrated early treatment with cyclic PMP can turn MoCD type A from a previously neonatal lethal condition with only palliative options, to near normal neurological outcomes in affected patients. We review MoCD and focus on describing the currently published evidence of this exciting new therapeutic option for MoCD type A caused by pathogenic variants in MOCD1. PMID:26653176

  8. sick: The Spectroscopic Inference Crank

    NASA Astrophysics Data System (ADS)

    Casey, Andrew R.

    2016-03-01

    There exists an inordinate amount of spectral data in both public and private astronomical archives that remain severely under-utilized. The lack of reliable open-source tools for analyzing large volumes of spectra contributes to this situation, which is poised to worsen as large surveys successively release orders of magnitude more spectra. In this article I introduce sick, the spectroscopic inference crank, a flexible and fast Bayesian tool for inferring astrophysical parameters from spectra. sick is agnostic to the wavelength coverage, resolving power, or general data format, allowing any user to easily construct a generative model for their data, regardless of its source. sick can be used to provide a nearest-neighbor estimate of model parameters, a numerically optimized point estimate, or full Markov Chain Monte Carlo sampling of the posterior probability distributions. This generality empowers any astronomer to capitalize on the plethora of published synthetic and observed spectra, and make precise inferences for a host of astrophysical (and nuisance) quantities. Model intensities can be reliably approximated from existing grids of synthetic or observed spectra using linear multi-dimensional interpolation, or a Cannon-based model. Additional phenomena that transform the data (e.g., redshift, rotational broadening, continuum, spectral resolution) are incorporated as free parameters and can be marginalized away. Outlier pixels (e.g., cosmic rays or poorly modeled regimes) can be treated with a Gaussian mixture model, and a noise model is included to account for systematically underestimated variance. Combining these phenomena into a scalar-justified, quantitative model permits precise inferences with credible uncertainties on noisy data. I describe the common model features, the implementation details, and the default behavior, which is balanced to be suitable for most astronomical applications. Using a forward model on low-resolution, high signal

  9. Adenylosuccinate lyase deficiency.

    PubMed

    Spiegel, Erin K; Colman, Roberta F; Patterson, David

    2006-01-01

    Adenylosuccinate lyase deficiency is a disease of purine metabolism which affects patients both biochemically and behaviorally. The symptoms are variable and include psychomotor retardation, autistic features, hypotonia, and seizures. Patients also accumulate the substrates of ADSL in body fluids. Both the presence of normal levels of ADSL enzyme activities in some patient tissues and the absence of a clear correlation between mutations, biochemistry, and behavior show that the system has unexplored biochemical and/or genetic complexity. It is unclear whether the pathological mechanisms of this disease result from a deficiency of purines, a toxicity of intermediates, or perturbation of another pathway or system. A patient with autistic features and mild psychomotor delay carries two novel mutations in this gene, E80D and D87E. The creation of a mouse model of this disease will be an important step in elucidating the in vivo mechanisms of the disease. Mice carrying mutations that cause ADSL deficiency in humans will be informative as to the effects of these mutations both during embryogenesis and on the brain, possibly leading to therapies for this disease in the future. PMID:16839792

  10. Primary antibody deficiency syndromes.

    PubMed

    Wood, P

    2009-03-01

    The primary antibody deficiency syndromes are a group of rare disorders characterized by an inability to produce clinically effective immunoglobulin responses. Some of these disorders result from genetic mutations in genes involved in B cell development, whereas others appear to be complex polygenic disorders. They most commonly present with recurrent infections due to encapsulated bacteria, although in the most common antibody deficiency, Common Variable Immunodeficiency, systemic and organ-specific autoimmunity can be a presenting feature. Diagnostic delay in this group of disorders remains a problem, and the laboratory has a vital role in the detection of abnormalities in immunoglobulin concentration and function. It is critical to distinguish this group of disorders from secondary causes of hypogammaglobulinaemia, in particular lymphoid malignancy, and appropriate laboratory investigations are of critical importance. Treatment of primary antibody deficiencies involves immunoglobulin replacement therapy, either via the intravenous or subcutaneous route. Patients remain at risk of a wide variety of complications, not all linked to diagnostic delay and inadequate therapy. In common variable immunodeficiency (CVID) in particular, patients remain at significantly increased risk of lymphoid malignancy, and regular clinical and laboratory monitoring is required. This review aims to give an overview of these conditions for the general reader, covering pathogenesis, clinical presentation, laboratory investigation, therapy and clinical management. PMID:19151170

  11. Iron-Deficiency Anemia (For Parents)

    MedlinePlus

    ... Things to Know About Zika & Pregnancy Iron-Deficiency Anemia KidsHealth > For Parents > Iron-Deficiency Anemia Print A ... common nutritional deficiency in children. About Iron-Deficiency Anemia Every red blood cell in the body contains ...

  12. Quantum Inference on Bayesian Networks

    NASA Astrophysics Data System (ADS)

    Yoder, Theodore; Low, Guang Hao; Chuang, Isaac

    2014-03-01

    Because quantum physics is naturally probabilistic, it seems reasonable to expect physical systems to describe probabilities and their evolution in a natural fashion. Here, we use quantum computation to speedup sampling from a graphical probability model, the Bayesian network. A specialization of this sampling problem is approximate Bayesian inference, where the distribution on query variables is sampled given the values e of evidence variables. Inference is a key part of modern machine learning and artificial intelligence tasks, but is known to be NP-hard. Classically, a single unbiased sample is obtained from a Bayesian network on n variables with at most m parents per node in time (nmP(e) - 1 / 2) , depending critically on P(e) , the probability the evidence might occur in the first place. However, by implementing a quantum version of rejection sampling, we obtain a square-root speedup, taking (n2m P(e) -1/2) time per sample. The speedup is the result of amplitude amplification, which is proving to be broadly applicable in sampling and machine learning tasks. In particular, we provide an explicit and efficient circuit construction that implements the algorithm without the need for oracle access.

  13. Bayesian Inference of Tumor Hypoxia

    NASA Astrophysics Data System (ADS)

    Gunawan, R.; Tenti, G.; Sivaloganathan, S.

    2009-12-01

    Tumor hypoxia is a state of oxygen deprivation in tumors. It has been associated with aggressive tumor phenotypes and with increased resistance to conventional cancer therapies. In this study, we report on the application of Bayesian sequential analysis in estimating the most probable value of tumor hypoxia quantification based on immunohistochemical assays of a biomarker. The `gold standard' of tumor hypoxia assessment is a direct measurement of pO2 in vivo by the Eppendorf polarographic electrode, which is an invasive technique restricted to accessible sites and living tissues. An attractive alternative is immunohistochemical staining to detect proteins expressed by cells during hypoxia. Carbonic anhydrase IX (CAIX) is an enzyme expressed on the cell membrane during hypoxia to balance the immediate extracellular microenvironment. CAIX is widely regarded as a surrogate marker of chronic hypoxia in various cancers. The study was conducted with two different experimental procedures. The first data set was a group of three patients with invasive cervical carcinomas, from which five biopsies were obtained. Each of the biopsies was fully sectioned and from each section, the proportion of CAIX-positive cells was estimated. Measurements were made by image analysis of multiple deep sections cut through these biopsies, labeled for CAIX using both immunofluorescence and immunohistochemical techniques [1]. The second data set was a group of 24 patients, also with invasive cervical carcinomas, from which two biopsies were obtained. Bayesian parameter estimation was applied to obtain a reliable inference about the proportion of CAIX-positive cells within the carcinomas, based on the available biopsies. From the first data set, two to three biopsies were found to be sufficient to infer the overall CAIX percentage in the simple form: best estimate±uncertainty. The second data-set led to a similar result in 70% of the cases. In the remaining cases Bayes' theorem warned us

  14. Carnitine palmitoyltransferase II deficiency

    PubMed Central

    Roe, C R.; Yang, B-Z; Brunengraber, H; Roe, D S.; Wallace, M; Garritson, B K.

    2008-01-01

    Background: Carnitine palmitoyltransferase II (CPT II) deficiency is an important cause of recurrent rhabdomyolysis in children and adults. Current treatment includes dietary fat restriction, with increased carbohydrate intake and exercise restriction to avoid muscle pain and rhabdomyolysis. Methods: CPT II enzyme assay, DNA mutation analysis, quantitative analysis of acylcarnitines in blood and cultured fibroblasts, urinary organic acids, the standardized 36-item Short-Form Health Status survey (SF-36) version 2, and bioelectric impedance for body fat composition. Diet treatment with triheptanoin at 30% to 35% of total daily caloric intake was used for all patients. Results: Seven patients with CPT II deficiency were studied from 7 to 61 months on the triheptanoin (anaplerotic) diet. Five had previous episodes of rhabdomyolysis requiring hospitalizations and muscle pain on exertion prior to the diet (two younger patients had not had rhabdomyolysis). While on the diet, only two patients experienced mild muscle pain with exercise. During short periods of noncompliance, two patients experienced rhabdomyolysis with exercise. None experienced rhabdomyolysis or hospitalizations while on the diet. All patients returned to normal physical activities including strenuous sports. Exercise restriction was eliminated. Previously abnormal SF-36 physical composite scores returned to normal levels that persisted for the duration of the therapy in all five symptomatic patients. Conclusions: The triheptanoin diet seems to be an effective therapy for adult-onset carnitine palmitoyltransferase II deficiency. GLOSSARY ALT = alanine aminotransferase; AST = aspartate aminotransferase; ATP = adenosine triphosphate; BHP = β-hydroxypentanoate; BKP = β-ketopentanoate; BKP-CoA = β-ketopentanoyl–coenzyme A; BUN = blood urea nitrogen; CAC = citric acid cycle; CoA = coenzyme A; CPK = creatine phosphokinase; CPT II = carnitine palmitoyltransferase II; LDL = low-density lipoprotein; MCT

  15. Iatrogenic nutritional deficiencies.

    PubMed

    Young, R C; Blass, J P

    1982-01-01

    This article catalogs the nutritional deficiencies inadvertently introduced by certain treatment regimens. Specifically, the iatrogenic effects on nutrition of surgery, hemodialysis, irradiation, and drugs are reviewed. Nutritional problems are particularly frequent consequences of surgery on the gastrointestinal tract. Gastric surgery can lead to deficiencies of vitamin B12, folate, iron, and thiamine, as well as to metabolic bone disease. The benefits of small bowel bypass are limited by the potentially severe nutritional consequences of this procedure. Following bypass surgery, patients should be monitored for signs of possible nutritional probems such as weight loss, neuropathy, cardiac arrhythmias, loss of stamina, or changes in mental status. Minimal laboratory tests should include hematologic evaluation, B12, folate, iron, albumin, calcium, phosphorus, alkaline phosphatase, transaminases, sodium, potassium, chloride, and carbon dioxide levels. Roentgenologic examination of the bone should also be obtained. Loss of bone substance is a major consequence of many forms of treatment, and dietary supplementation with calcium is warranted. Patients undergoing hemodialysis have shown carnitine and choline deficiencies, potassium depletion, and hypovitaminosis, as well as osteomalacia. Chronic drug use may alter intake, synthesis, absorption, transport, storage, metabolism, or excretion of nutrients. Patients vary markedly in the metabolic effects of drugs, and recommendations for nutrition must be related to age, sex, reproductive status, and genetic endowment. Moreover, the illness being treated can itself alter nutritional requirements and the effect of the treatment on nutrient status. The changes in nutritional levels induced by use of estrogen-containing oral contraceptives (OCs) are obscure; however, the effects on folate matabolism appear to be of less clinical import than previously suggested. Reduction in pyridoxine and serum vitamin B12 levels has been

  16. Treatment of carnitine deficiency.

    PubMed

    Winter, S C

    2003-01-01

    Carnitine deficiency is a secondary complication of many inborn errors of metabolism. Pharmacological treatment with carnitine not only corrects the deficiency, it facilitates removal of accumulating toxic acyl intermediates and the generation of mitochondrial free coenzyme A (CoA). The United States Food and Drug Administration (US FDA) approved the use of carnitine for the treatment of inborn errors of metabolism in 1992. This approval was based on retrospective chart analysis of 90 patients, with 18 in the untreated cohort and 72 in the treated cohort. Efficacy was evaluated on the basis of clinical and biochemical findings. Compelling data included increased excretion of disease-specific acylcarnitine derivatives in a dose-response relationship, decreased levels of metabolites in the blood, and improved clinical status with decreased hospitalization frequency, improved growth and significantly lower mortality rates as compared to historical controls. Complications of carnitine treatment were few, with gastrointestinal disturbances and odour being the most frequent. No laboratory or clinical safety issues were identified. Intravenous carnitine preparations were also approved for treatment of secondary carnitine deficiency. Since only 25% of enteral carnitine is absorbed and gastrointestinal tolerance of high doses is poor, parenteral carnitine treatment is an appealing alternative therapeutic approach. In 7 patients treated long term with high-dose weekly to daily venous boluses of parenteral carnitine through a subcutaneous venous port, benefits included decreased frequency of decompensations, improved growth, improved muscle strength and decreased reliance on medical foods with liberalization of protein intake. Port infections were the most troubling complication. Theoretical concerns continue to be voiced that carnitine might result in fatal arrhythmias in patients with long-chain fat metabolism defects. No published clinical studies substantiate these

  17. Infering Networks From Collective Dynamics

    NASA Astrophysics Data System (ADS)

    Timme, Marc

    How can we infer direct physical interactions between pairs of units from only knowing the units' time series? Here we present a dynamical systems' view on collective network dynamics, and propose the concept of a dynamics' space to reveal interaction networks from time series. We present two examples: one, where the time series stem from standard ordinary differential equations, and a second, more abstract, where the time series exhibits only partial information about the units' states. We apply the latter to neural circuit dynamics where the observables are spike timing data, i.e. only a discrete, state-dependent outputs of the neurons. These results may help revealing network structure for systems where direct access to dynamics is simpler than to connectivity, cf.. This is work with Jose Casadiego, Srinivas Gorur Shandilya, Mor Nitzan, Hauke Haehne and Dimitra Maoutsa. Supported by Grants of the BMBF (Future Compliant Power Grids - CoNDyNet) and by the Max Planck Society to MT.

  18. Inferred properties of stellar granulation

    SciTech Connect

    Gray, D.F.; Toner, C.G.

    1985-06-01

    Apparent characteristics of stellar granulation in F and G main-sequence stars are inferred directly from observed spectral-line asymmetries and from comparisons of numerical simulations with the observations: (1) the apparent granulation velocity increases with effective temperature, (2) the dispersion of granule velocities about their mean velocity of rise increases with the apparent granulation velocity, (3) the mean velocity of rise of granules must be less than the total line broadening, (4) the apparent velocity difference between granules and dark lanes corresponds to the granulation velocity deduced from stellar line bisectors, (5) the dark lanes show velocities of fall approximately twice as large as the granule rise velocities, (6) the light contributed to the stellar flux by the granules is four to ten times more than the light from the dark lanes. Stellar rotation is predicted to produce distortions in the line bisectors which may give information on the absolute velocity displacements of the line bisectors. 37 references.

  19. Structural inference for uncertain networks

    NASA Astrophysics Data System (ADS)

    Martin, Travis; Ball, Brian; Newman, M. E. J.

    2016-01-01

    In the study of networked systems such as biological, technological, and social networks the available data are often uncertain. Rather than knowing the structure of a network exactly, we know the connections between nodes only with a certain probability. In this paper we develop methods for the analysis of such uncertain data, focusing particularly on the problem of community detection. We give a principled maximum-likelihood method for inferring community structure and demonstrate how the results can be used to make improved estimates of the true structure of the network. Using computer-generated benchmark networks we demonstrate that our methods are able to reconstruct known communities more accurately than previous approaches based on data thresholding. We also give an example application to the detection of communities in a protein-protein interaction network.

  20. Antithrombin deficiency in pregnancy.

    PubMed

    Durai, Shivani; Tan, Lay Kok; Lim, Serene

    2016-01-01

    We present a case of a 39-year-old, gravida 3 para 2, Chinese female with a history of inherited type 1 Antithrombin deficiency and multiple prior episodes of venous thromboembolism. She presented at 29+4 weeks' gestation with severe pre-eclampsia complicated by haemolysis, elevated liver enzymes and low platelet (HELLP) syndrome. She subsequently underwent an emergency caesarean section for non-reassuring fetal status, which was complicated by postpartum haemorrhage secondary to uterine atony, requiring a B-Lynch suture intraoperatively. PMID:27207982

  1. Nasal Tip Deficiency.

    PubMed

    Cerkes, Nazim

    2016-01-01

    Nasal tip deficiency can be congenital or secondary to previous nasal surgeries. Underdeveloped medial crura usually present with underprojected tip and lack of tip definition. Weakness or malposition of lateral crura causes alar rim retraction and lateral nasal wall weakness. Structural grafting of alar cartilages strengthens the tip framework, reinforces the disrupted support mechanisms, and controls the position of the nasal tip. In secondary cases, anatomic reconstruction of the weakened or interrupted alar cartilages and reconstitution of a stable nasal tip tripod must be the goal for a predictable outcome. PMID:26616702

  2. Disialotransferrin developmental deficiency syndrome.

    PubMed Central

    Kristiansson, B; Andersson, M; Tonnby, B; Hagberg, B

    1989-01-01

    Seven mentally deficient children and adolescents (three pairs of siblings and one singleton) were studied. A peculiar external appearance, a characteristic neurohepatosubcutaneous tissue impairment syndrome and, as a biological marker, an abnormal sialic acid transferrin pattern were characteristic features. All seven seemed odd from birth and prone to acute cerebral dysfunction during catabolic states. Abnormal lower neurone, cerebellar, and retinal functions dominated from later childhood. The disialotransferrin pattern found in serum and cerebrospinal fluid is thought to be the biological marker of a newly discovered inborn error of glycoprotein metabolism with autosomal recessive inheritance. Images Fig 1 Fig 2 p74-b PMID:2466439

  3. Transdimensional inference in the geosciences.

    PubMed

    Sambridge, M; Bodin, T; Gallagher, K; Tkalcic, H

    2013-02-13

    Seismologists construct images of the Earth's interior structure using observations, derived from seismograms, collected at the surface. A common approach to such inverse problems is to build a single 'best' Earth model, in some sense. This is despite the fact that the observations by themselves often do not require, or even allow, a single best-fit Earth model to exist. Interpretation of optimal models can be fraught with difficulties, particularly when formal uncertainty estimates become heavily dependent on the regularization imposed. Similar issues occur across the physical sciences with model construction in ill-posed problems. An alternative approach is to embrace the non-uniqueness directly and employ an inference process based on parameter space sampling. Instead of seeking a best model within an optimization framework, one seeks an ensemble of solutions and derives properties of that ensemble for inspection. While this idea has itself been employed for more than 30 years, it is now receiving increasing attention in the geosciences. Recently, it has been shown that transdimensional and hierarchical sampling methods have some considerable benefits for problems involving multiple parameter types, uncertain data errors and/or uncertain model parametrizations, as are common in seismology. Rather than being forced to make decisions on parametrization, the level of data noise and the weights between data types in advance, as is often the case in an optimization framework, the choice can be informed by the data themselves. Despite the relatively high computational burden involved, the number of areas where sampling methods are now feasible is growing rapidly. The intention of this article is to introduce concepts of transdimensional inference to a general readership and illustrate with particular seismological examples. A growing body of references provide necessary detail. PMID:23277604

  4. Selenium deficiency mitigates hypothyroxinemia in iodine-deficient subjects.

    PubMed

    Vanderpas, J B; Contempré, B; Duale, N L; Deckx, H; Bebe, N; Longombé, A O; Thilly, C H; Diplock, A T; Dumont, J E

    1993-02-01

    Studies were performed to assess the role of combined selenium and iodine deficiency in the etiology of endemic myxedematous cretinism in a population in Zaire. One effect of selenium deficiency may be to lower glutathione peroxidase activity in the thyroid gland, thus allowing hydrogen peroxide produced during thyroid hormone synthesis to be cytotoxic. In selenium-and-iodine-deficient humans, selenium supplementation may aggravate hypothyroidism by stimulating thyroxin metabolism by the selenoenzyme type I iodothyronine 5'-deiodinase. Selenium supplementation is thus not indicated without iodine or thyroid hormone supplementation in cases of combined selenium and iodine deficiencies. PMID:8427203

  5. Bayesian Nonparametric Inference – Why and How

    PubMed Central

    Müller, Peter; Mitra, Riten

    2013-01-01

    We review inference under models with nonparametric Bayesian (BNP) priors. The discussion follows a set of examples for some common inference problems. The examples are chosen to highlight problems that are challenging for standard parametric inference. We discuss inference for density estimation, clustering, regression and for mixed effects models with random effects distributions. While we focus on arguing for the need for the flexibility of BNP models, we also review some of the more commonly used BNP models, thus hopefully answering a bit of both questions, why and how to use BNP. PMID:24368932

  6. Inference engine using optical array logic

    NASA Astrophysics Data System (ADS)

    Iwata, Masaya; Tanida, Jun; Ichioka, Yoshiki

    1990-07-01

    An implementation method for an inference engine using optical array logic is presented. Optical array logic is a technique for parallel neighborhood operation using spatial coding and 2-D correlation. For efficient execution of inference in artificial intelligence problems, a large number of data must be searched effectively. To achieve this demand, a template matching technique is applied to the inference operation. By introducing a new function of data conversion, the inference operation can be implemented with optical array logic, which utilizes parallelism in optical techniques.

  7. Iron deficiency in pregnancy

    PubMed Central

    McMahon, Lawrence P

    2010-01-01

    Iron deficiency (ID) and related anaemia (IDA) during pregnancy are highly prevalent worldwide in both developed and developing nations although the causes are often different. At conception, many women lack sufficient iron stores to meet the increased requirements of pregnancy, which are calculated at approximately 1200 mg. Appraisal of iron status in pregnant women is problematic, however the most reliable available diagnostic test is a serum ferritin < 20 µg/L. ID is often associated with other nutritional disorders, and there is frequently a secondary cause or association. A greater oral intake is usually insufficient to meet the increased demands of pregnancy, however regular oral supplements (given either daily or intermittently) can often meet maternal needs and avoid associated neonatal complications of IDA. Over-treatment with iron should be avoided, but intravenous administration is useful when deficiency is discovered late, is severe, or if the woman is intolerant of oral formulations. This paper reviews the current literature, and addresses differences in the prevalence and causes of ID betwen developed and developing nations. It examines gestational iron requirements, distinguishes between ID and IDA, and highlights difficulties in diagnostic testing. Finally, it appraises the evidence for and against different treatment regimens, ranging from food fortification to intravenous iron infusions, according to availability and to need.

  8. Vitamin D Deficiency

    PubMed Central

    Alshishtawy, Moeness Moustafa

    2012-01-01

    Recently, scientists have generated a strong body of evidence providing new information about the preventive effect of vitamin D on a broad range of disorders. This evidence suggests that vitamin D is much more than a nutrient needed for bone health; it is an essential hormone required for regulation of a large number of physiological functions. Sufficient concentration of serum 25-hydroxyvitamin D is essential for optimising human health. This article reviews the present state-of-the-art knowledge about vitamin D’s status worldwide and refers to recent articles discussing some of the general background of vitamin D, including sources, benefits, deficiencies, and dietary requirements, especially in pregnancy. They offer evidence that vitamin D deficiency could be a major public health burden in many parts of the world, mostly because of sun deprivation. The article also discusses the debate about optimal concentration of circulating serum 25-hydroxyvitamin D, and explores different views on the amount of vitamin D supplementation required to achieve and maintain this concentration. PMID:22548132

  9. Glucose-6-phosphatase deficiency

    PubMed Central

    2011-01-01

    Glucose-6-phosphatase deficiency (G6P deficiency), or glycogen storage disease type I (GSDI), is a group of inherited metabolic diseases, including types Ia and Ib, characterized by poor tolerance to fasting, growth retardation and hepatomegaly resulting from accumulation of glycogen and fat in the liver. Prevalence is unknown and annual incidence is around 1/100,000 births. GSDIa is the more frequent type, representing about 80% of GSDI patients. The disease commonly manifests, between the ages of 3 to 4 months by symptoms of hypoglycemia (tremors, seizures, cyanosis, apnea). Patients have poor tolerance to fasting, marked hepatomegaly, growth retardation (small stature and delayed puberty), generally improved by an appropriate diet, osteopenia and sometimes osteoporosis, full-cheeked round face, enlarged kydneys and platelet dysfunctions leading to frequent epistaxis. In addition, in GSDIb, neutropenia and neutrophil dysfunction are responsible for tendency towards infections, relapsing aphtous gingivostomatitis, and inflammatory bowel disease. Late complications are hepatic (adenomas with rare but possible transformation into hepatocarcinoma) and renal (glomerular hyperfiltration leading to proteinuria and sometimes to renal insufficiency). GSDI is caused by a dysfunction in the G6P system, a key step in the regulation of glycemia. The deficit concerns the catalytic subunit G6P-alpha (type Ia) which is restricted to expression in the liver, kidney and intestine, or the ubiquitously expressed G6P transporter (type Ib). Mutations in the genes G6PC (17q21) and SLC37A4 (11q23) respectively cause GSDIa and Ib. Many mutations have been identified in both genes,. Transmission is autosomal recessive. Diagnosis is based on clinical presentation, on abnormal basal values and absence of hyperglycemic response to glucagon. It can be confirmed by demonstrating a deficient activity of a G6P system component in a liver biopsy. To date, the diagnosis is most commonly confirmed

  10. Zinc deficiency and eating disorders.

    PubMed

    Humphries, L; Vivian, B; Stuart, M; McClain, C J

    1989-12-01

    Decreased food intake, a cyclic pattern of eating, and weight loss are major manifestations of zinc deficiency. In this study, zinc status was evaluated in 62 patients with bulimia and 24 patients with anorexia nervosa. Forty percent of patients with bulimia and 54% of those with anorexia nervosa had biochemical evidence of zinc deficiency. The authors suggest that for a variety of reasons, such as lower dietary intake of zinc, impaired zinc absorption, vomiting, diarrhea, and binging on low-zinc foods, patients with eating disorders may develop zinc deficiency. This acquired zinc deficiency could then add to the chronicity of altered eating behavior in those patients. PMID:2600063

  11. Protein inference: A protein quantification perspective.

    PubMed

    He, Zengyou; Huang, Ting; Liu, Xiaoqing; Zhu, Peijun; Teng, Ben; Deng, Shengchun

    2016-08-01

    In mass spectrometry-based shotgun proteomics, protein quantification and protein identification are two major computational problems. To quantify the protein abundance, a list of proteins must be firstly inferred from the raw data. Then the relative or absolute protein abundance is estimated with quantification methods, such as spectral counting. Until now, most researchers have been dealing with these two processes separately. In fact, the protein inference problem can be regarded as a special protein quantification problem in the sense that truly present proteins are those proteins whose abundance values are not zero. Some recent published papers have conceptually discussed this possibility. However, there is still a lack of rigorous experimental studies to test this hypothesis. In this paper, we investigate the feasibility of using protein quantification methods to solve the protein inference problem. Protein inference methods aim to determine whether each candidate protein is present in the sample or not. Protein quantification methods estimate the abundance value of each inferred protein. Naturally, the abundance value of an absent protein should be zero. Thus, we argue that the protein inference problem can be viewed as a special protein quantification problem in which one protein is considered to be present if its abundance is not zero. Based on this idea, our paper tries to use three simple protein quantification methods to solve the protein inference problem effectively. The experimental results on six data sets show that these three methods are competitive with previous protein inference algorithms. This demonstrates that it is plausible to model the protein inference problem as a special protein quantification task, which opens the door of devising more effective protein inference algorithms from a quantification perspective. The source codes of our methods are available at: http://code.google.com/p/protein-inference/. PMID:26935399

  12. Forward and Backward Inference in Spatial Cognition

    PubMed Central

    Penny, Will D.; Zeidman, Peter; Burgess, Neil

    2013-01-01

    This paper shows that the various computations underlying spatial cognition can be implemented using statistical inference in a single probabilistic model. Inference is implemented using a common set of ‘lower-level’ computations involving forward and backward inference over time. For example, to estimate where you are in a known environment, forward inference is used to optimally combine location estimates from path integration with those from sensory input. To decide which way to turn to reach a goal, forward inference is used to compute the likelihood of reaching that goal under each option. To work out which environment you are in, forward inference is used to compute the likelihood of sensory observations under the different hypotheses. For reaching sensory goals that require a chaining together of decisions, forward inference can be used to compute a state trajectory that will lead to that goal, and backward inference to refine the route and estimate control signals that produce the required trajectory. We propose that these computations are reflected in recent findings of pattern replay in the mammalian brain. Specifically, that theta sequences reflect decision making, theta flickering reflects model selection, and remote replay reflects route and motor planning. We also propose a mapping of the above computational processes onto lateral and medial entorhinal cortex and hippocampus. PMID:24348230

  13. Inferring Learners' Knowledge from Their Actions

    ERIC Educational Resources Information Center

    Rafferty, Anna N.; LaMar, Michelle M.; Griffiths, Thomas L.

    2015-01-01

    Watching another person take actions to complete a goal and making inferences about that person's knowledge is a relatively natural task for people. This ability can be especially important in educational settings, where the inferences can be used for assessment, diagnosing misconceptions, and providing informative feedback. In this paper, we…

  14. Local and Global Thinking in Statistical Inference

    ERIC Educational Resources Information Center

    Pratt, Dave; Johnston-Wilder, Peter; Ainley, Janet; Mason, John

    2008-01-01

    In this reflective paper, we explore students' local and global thinking about informal statistical inference through our observations of 10- to 11-year-olds, challenged to infer the unknown configuration of a virtual die, but able to use the die to generate as much data as they felt necessary. We report how they tended to focus on local changes…

  15. The Impact of Disablers on Predictive Inference

    ERIC Educational Resources Information Center

    Cummins, Denise Dellarosa

    2014-01-01

    People consider alternative causes when deciding whether a cause is responsible for an effect (diagnostic inference) but appear to neglect them when deciding whether an effect will occur (predictive inference). Five experiments were conducted to test a 2-part explanation of this phenomenon: namely, (a) that people interpret standard predictive…

  16. Causal Inferences during Text Comprehension and Production.

    ERIC Educational Resources Information Center

    Kemper, Susan

    As comprehension failure results whenever readers are unable to infer missing causal connections, recent comprehension research has focused both on assessing the inferential complexity of texts and on investigating students' developing ability to infer causal relationships. Studies have demonstrated that texts rely on four types of causal…

  17. Scalar Inferences in Autism Spectrum Disorders

    ERIC Educational Resources Information Center

    Chevallier, Coralie; Wilson, Deirdre; Happe, Francesca; Noveck, Ira

    2010-01-01

    On being told "John or Mary will come", one might infer that "not both" of them will come. Yet the semantics of "or" is compatible with a situation where both John and Mary come. Inferences of this type, which enrich the semantics of "or" from an "inclusive" to an "exclusive" interpretation, have been extensively studied in linguistic pragmatics.…

  18. Genetic Network Inference Using Hierarchical Structure.

    PubMed

    Kimura, Shuhei; Tokuhisa, Masato; Okada-Hatakeyama, Mariko

    2016-01-01

    Many methods for inferring genetic networks have been proposed, but the regulations they infer often include false-positives. Several researchers have attempted to reduce these erroneous regulations by proposing the use of a priori knowledge about the properties of genetic networks such as their sparseness, scale-free structure, and so on. This study focuses on another piece of a priori knowledge, namely, that biochemical networks exhibit hierarchical structures. Based on this idea, we propose an inference approach that uses the hierarchical structure in a target genetic network. To obtain a reasonable hierarchical structure, the first step of the proposed approach is to infer multiple genetic networks from the observed gene expression data. We take this step using an existing method that combines a genetic network inference method with a bootstrap method. The next step is to extract a hierarchical structure from the inferred networks that is consistent with most of the networks. Third, we use the hierarchical structure obtained to assign confidence values to all candidate regulations. Numerical experiments are also performed to demonstrate the effectiveness of using the hierarchical structure in the genetic network inference. The improvement accomplished by the use of the hierarchical structure is small. However, the hierarchical structure could be used to improve the performances of many existing inference methods. PMID:26941653

  19. The Reasoning behind Informal Statistical Inference

    ERIC Educational Resources Information Center

    Makar, Katie; Bakker, Arthur; Ben-Zvi, Dani

    2011-01-01

    Informal statistical inference (ISI) has been a frequent focus of recent research in statistics education. Considering the role that context plays in developing ISI calls into question the need to be more explicit about the reasoning that underpins ISI. This paper uses educational literature on informal statistical inference and philosophical…

  20. Reinforcement learning or active inference?

    PubMed

    Friston, Karl J; Daunizeau, Jean; Kiebel, Stefan J

    2009-01-01

    This paper questions the need for reinforcement learning or control theory when optimising behaviour. We show that it is fairly simple to teach an agent complicated and adaptive behaviours using a free-energy formulation of perception. In this formulation, agents adjust their internal states and sampling of the environment to minimize their free-energy. Such agents learn causal structure in the environment and sample it in an adaptive and self-supervised fashion. This results in behavioural policies that reproduce those optimised by reinforcement learning and dynamic programming. Critically, we do not need to invoke the notion of reward, value or utility. We illustrate these points by solving a benchmark problem in dynamic programming; namely the mountain-car problem, using active perception or inference under the free-energy principle. The ensuing proof-of-concept may be important because the free-energy formulation furnishes a unified account of both action and perception and may speak to a reappraisal of the role of dopamine in the brain. PMID:19641614

  1. Reinforcement Learning or Active Inference?

    PubMed Central

    Friston, Karl J.; Daunizeau, Jean; Kiebel, Stefan J.

    2009-01-01

    This paper questions the need for reinforcement learning or control theory when optimising behaviour. We show that it is fairly simple to teach an agent complicated and adaptive behaviours using a free-energy formulation of perception. In this formulation, agents adjust their internal states and sampling of the environment to minimize their free-energy. Such agents learn causal structure in the environment and sample it in an adaptive and self-supervised fashion. This results in behavioural policies that reproduce those optimised by reinforcement learning and dynamic programming. Critically, we do not need to invoke the notion of reward, value or utility. We illustrate these points by solving a benchmark problem in dynamic programming; namely the mountain-car problem, using active perception or inference under the free-energy principle. The ensuing proof-of-concept may be important because the free-energy formulation furnishes a unified account of both action and perception and may speak to a reappraisal of the role of dopamine in the brain. PMID:19641614

  2. Causal Inference in Public Health

    PubMed Central

    Glass, Thomas A.; Goodman, Steven N.; Hernán, Miguel A.; Samet, Jonathan M.

    2014-01-01

    Causal inference has a central role in public health; the determination that an association is causal indicates the possibility for intervention. We review and comment on the long-used guidelines for interpreting evidence as supporting a causal association and contrast them with the potential outcomes framework that encourages thinking in terms of causes that are interventions. We argue that in public health this framework is more suitable, providing an estimate of an action’s consequences rather than the less precise notion of a risk factor’s causal effect. A variety of modern statistical methods adopt this approach. When an intervention cannot be specified, causal relations can still exist, but how to intervene to change the outcome will be unclear. In application, the often-complex structure of causal processes needs to be acknowledged and appropriate data collected to study them. These newer approaches need to be brought to bear on the increasingly complex public health challenges of our globalized world. PMID:23297653

  3. Active inference and epistemic value.

    PubMed

    Friston, Karl; Rigoli, Francesco; Ognibene, Dimitri; Mathys, Christoph; Fitzgerald, Thomas; Pezzulo, Giovanni

    2015-01-01

    We offer a formal treatment of choice behavior based on the premise that agents minimize the expected free energy of future outcomes. Crucially, the negative free energy or quality of a policy can be decomposed into extrinsic and epistemic (or intrinsic) value. Minimizing expected free energy is therefore equivalent to maximizing extrinsic value or expected utility (defined in terms of prior preferences or goals), while maximizing information gain or intrinsic value (or reducing uncertainty about the causes of valuable outcomes). The resulting scheme resolves the exploration-exploitation dilemma: Epistemic value is maximized until there is no further information gain, after which exploitation is assured through maximization of extrinsic value. This is formally consistent with the Infomax principle, generalizing formulations of active vision based upon salience (Bayesian surprise) and optimal decisions based on expected utility and risk-sensitive (Kullback-Leibler) control. Furthermore, as with previous active inference formulations of discrete (Markovian) problems, ad hoc softmax parameters become the expected (Bayes-optimal) precision of beliefs about, or confidence in, policies. This article focuses on the basic theory, illustrating the ideas with simulations. A key aspect of these simulations is the similarity between precision updates and dopaminergic discharges observed in conditioning paradigms. PMID:25689102

  4. Inference-based constraint satisfaction supports explanation

    SciTech Connect

    Sqalli, M.H.; Freuder, E.C.

    1996-12-31

    Constraint satisfaction problems are typically solved using search, augmented by general purpose consistency inference methods. This paper proposes a paradigm shift in which inference is used as the primary problem solving method, and attention is focused on special purpose, domain specific inference methods. While we expect this approach to have computational advantages, we emphasize here the advantages of a solution method that is more congenial to human thought processes. Specifically we use inference-based constraint satisfaction to support explanations of the problem solving behavior that are considerably more meaningful than a trace of a search process would be. Logic puzzles are used as a case study. Inference-based constraint satisfaction proves surprisingly powerful and easily extensible in this domain. Problems drawn from commercial logic puzzle booklets are used for evaluation. Explanations are produced that compare well with the explanations provided by these booklets.

  5. Principal stratification in causal inference.

    PubMed

    Frangakis, Constantine E; Rubin, Donald B

    2002-03-01

    Many scientific problems require that treatment comparisons be adjusted for posttreatment variables, but the estimands underlying standard methods are not causal effects. To address this deficiency, we propose a general framework for comparing treatments adjusting for posttreatment variables that yields principal effects based on principal stratification. Principal stratification with respect to a posttreatment variable is a cross-classification of subjects defined by the joint potential values of that posttreatment variable tinder each of the treatments being compared. Principal effects are causal effects within a principal stratum. The key property of principal strata is that they are not affected by treatment assignment and therefore can be used just as any pretreatment covariate. such as age category. As a result, the central property of our principal effects is that they are always causal effects and do not suffer from the complications of standard posttreatment-adjusted estimands. We discuss briefly that such principal causal effects are the link between three recent applications with adjustment for posttreatment variables: (i) treatment noncompliance, (ii) missing outcomes (dropout) following treatment noncompliance. and (iii) censoring by death. We then attack the problem of surrogate or biomarker endpoints, where we show, using principal causal effects, that all current definitions of surrogacy, even when perfectly true, do not generally have the desired interpretation as causal effects of treatment on outcome. We go on to forrmulate estimands based on principal stratification and principal causal effects and show their superiority. PMID:11890317

  6. Basic Skills: Dealing with Deficiencies.

    ERIC Educational Resources Information Center

    New Mexico State Univ., Las Cruces.

    Research findings on college instruction and basic skills deficiencies are discussed in 12 papers from the first Regional Conference on University Teaching. Titles and authors are as follows: "Basic Skills: Dealing with Deficiencies" (Susanne D. Roueche, with responses by Gary B. Donart, Betty Harris, and James Nordyke); "Is Higher Education an…

  7. Iron deficiency anemia in children.

    PubMed

    Subramaniam, Girish; Girish, Meenakshi

    2015-06-01

    Iron deficiency is not just anemia; it can be responsible for a long list of other manifestations. This topic is of great importance, especially in infancy and early childhood, for a variety of reasons. Firstly, iron need is maximum in this period. Secondly, diet in infancy is usually deficient in iron. Thirdly and most importantly, iron deficiency at this age can result in neurodevelopmental and cognitive deficits, which may not be reversible. Hypochromia and microcytosis in a complete blood count (CBC) makes iron deficiency anemia (IDA) most likely diagnosis. Absence of response to iron should make us look for other differential diagnosis like β thalassemia trait and anemia of chronic disease. Celiac disease is the most important cause of true IDA not responding to oral iron therapy. While oral ferrous sulphate is the cheapest and most effective therapy for IDA, simple nonpharmacological and pharmacological measures can go a long way in prevention of iron deficiency. PMID:25636824

  8. Interactions between copper deficiency, selenium deficiency and adriamycin toxicity

    SciTech Connect

    Fischer, J.; Tackett, R.; Johnson, M.A. )

    1991-03-15

    The objective of this study was to test the hypothesis that there are interactions between copper (Cu) and selenium (Se) status, and adriamycin (ADR) toxicity. Male Sprague Dawley rats were fed Cu,Se adequate; Cu deficient, Se adequate ({minus}Cu); Cu adequate, Se deficient; or Cu,Se deficient diets for 38-41 days. ADR or saline (SAL) were administered weekly for the last 4 weeks of the study. Cu deficiency was confirmed by a 3-fold decrease in liver Cu,Zn-superoxide dismutase and liver Cu, and a 5-fold decrease in RBC Cu,Zn-SOD. Se deficiency was confirmed by a 10-fold decrease in liver glutathione peroxidase (GSH-Px). ADR, Cu deficiency and Se deficiency all caused EKG abnormalities. However, Cu and Se deficiencies did not enhance ADR's influence on EKGs. ADR increased lipid peroxidation in liver by 15% and in heart by 18% (NS). Cu deficiency decreased ADR-induced lipid peroxidation in heart tissue by 25%. ADR influenced Se status by significantly increasing heart GSH-Px, and Cu status by increasing liver Cu, plasma ceruloplasmin and liver Cu, Zn-SOD. These elevations in Cu,Zn-SOD and GSH-Px may be a consequence of the increased lipid peroxidation initiated by ADR. In {minus}Cu rats, ADR caused severe hemolytic anemia characterized by a 19% decrease in hematocrit and a 17-fold increase in splenic Fe. These data suggest that there are numerous interactions between ADR toxicity and Cu and Se status.

  9. Inferring genetic networks from microarray data.

    SciTech Connect

    May, Elebeoba Eni; Davidson, George S.; Martin, Shawn Bryan; Werner-Washburne, Margaret C.; Faulon, Jean-Loup Michel

    2004-06-01

    In theory, it should be possible to infer realistic genetic networks from time series microarray data. In practice, however, network discovery has proved problematic. The three major challenges are: (1) inferring the network; (2) estimating the stability of the inferred network; and (3) making the network visually accessible to the user. Here we describe a method, tested on publicly available time series microarray data, which addresses these concerns. The inference of genetic networks from genome-wide experimental data is an important biological problem which has received much attention. Approaches to this problem have typically included application of clustering algorithms [6]; the use of Boolean networks [12, 1, 10]; the use of Bayesian networks [8, 11]; and the use of continuous models [21, 14, 19]. Overviews of the problem and general approaches to network inference can be found in [4, 3]. Our approach to network inference is similar to earlier methods in that we use both clustering and Boolean network inference. However, we have attempted to extend the process to better serve the end-user, the biologist. In particular, we have incorporated a system to assess the reliability of our network, and we have developed tools which allow interactive visualization of the proposed network.

  10. Linguistic Markers of Inference Generation While Reading.

    PubMed

    Clinton, Virginia; Carlson, Sarah E; Seipel, Ben

    2016-06-01

    Words can be informative linguistic markers of psychological constructs. The purpose of this study is to examine associations between word use and the process of making meaningful connections to a text while reading (i.e., inference generation). To achieve this purpose, think-aloud data from third-fifth grade students ([Formula: see text]) reading narrative texts were hand-coded for inferences. These data were also processed with a computer text analysis tool, Linguistic Inquiry and Word Count, for percentages of word use in the following categories: cognitive mechanism words, nonfluencies, and nine types of function words. Findings indicate that cognitive mechanisms were an independent, positive predictor of connections to background knowledge (i.e., elaborative inference generation) and nonfluencies were an independent, negative predictor of connections within the text (i.e., bridging inference generation). Function words did not provide unique variance towards predicting inference generation. These findings are discussed in the context of a cognitive reflection model and the differences between bridging and elaborative inference generation. In addition, potential practical implications for intelligent tutoring systems and computer-based methods of inference identification are presented. PMID:25833811

  11. Statistical Physics of High Dimensional Inference

    NASA Astrophysics Data System (ADS)

    Advani, Madhu; Ganguli, Surya

    To model modern large-scale datasets, we need efficient algorithms to infer a set of P unknown model parameters from N noisy measurements. What are fundamental limits on the accuracy of parameter inference, given limited measurements, signal-to-noise ratios, prior information, and computational tractability requirements? How can we combine prior information with measurements to achieve these limits? Classical statistics gives incisive answers to these questions as the measurement density α =N/P --> ∞ . However, modern high-dimensional inference problems, in fields ranging from bio-informatics to economics, occur at finite α. We formulate and analyze high-dimensional inference analytically by applying the replica and cavity methods of statistical physics where data serves as quenched disorder and inferred parameters play the role of thermal degrees of freedom. Our analysis reveals that widely cherished Bayesian inference algorithms such as maximum likelihood and maximum a posteriori are suboptimal in the modern setting, and yields new tractable, optimal algorithms to replace them as well as novel bounds on the achievable accuracy of a large class of high-dimensional inference algorithms. Thanks to Stanford Graduate Fellowship and Mind Brain Computation IGERT grant for support.

  12. Genetics Home Reference: glucose phosphate isomerase deficiency

    MedlinePlus

    ... Me Understand Genetics Home Health Conditions GPI deficiency glucose phosphate isomerase deficiency Enable Javascript to view the ... boxes. Download PDF Open All Close All Description Glucose phosphate isomerase (GPI) deficiency is an inherited disorder ...

  13. Genetics Home Reference: adenosine deaminase 2 deficiency

    MedlinePlus

    ... Health Conditions adenosine deaminase 2 deficiency adenosine deaminase 2 deficiency Enable Javascript to view the expand/collapse ... PDF Open All Close All Description Adenosine deaminase 2 (ADA2) deficiency is a disorder characterized by abnormal ...

  14. What Causes Alpha-1 Antitrypsin Deficiency?

    MedlinePlus

    ... from the NHLBI on Twitter. What Causes Alpha-1 Antitrypsin Deficiency? Alpha-1 antitrypsin (AAT) deficiency is an inherited disease. "Inherited" ... have AAT deficiency inherit two faulty AAT genes, one from each parent. These genes tell cells in ...

  15. Monocular Elevation Deficiency - Double Elevator Palsy

    MedlinePlus

    ... Español Condiciones Chinese Conditions Monocular Elevation Deficiency/ Double Elevator Palsy En Español Read in Chinese What is monocular elevation deficiency (Double Elevator Palsy)? Monocular Elevation Deficiency, also known by the ...

  16. Genetics Home Reference: protein C deficiency

    MedlinePlus

    ... Understand Genetics Home Health Conditions protein C deficiency protein C deficiency Enable Javascript to view the expand/ ... boxes. Download PDF Open All Close All Description Protein C deficiency is a disorder that increases the ...

  17. Genetics Home Reference: protein S deficiency

    MedlinePlus

    ... Me Understand Genetics Home Health Conditions protein S deficiency protein S deficiency Enable Javascript to view the expand/collapse boxes. Download PDF Open All Close All Description Protein S deficiency is a disorder of blood clotting. People ...

  18. Genetics Home Reference: factor V deficiency

    MedlinePlus

    ... Genetics Home Health Conditions factor V deficiency factor V deficiency Enable Javascript to view the expand/collapse ... Download PDF Open All Close All Description Factor V deficiency is a rare bleeding disorder. The signs ...

  19. Genetics Home Reference: isolated growth hormone deficiency

    MedlinePlus

    ... Health Conditions isolated growth hormone deficiency isolated growth hormone deficiency Enable Javascript to view the expand/collapse ... PDF Open All Close All Description Isolated growth hormone deficiency is a condition caused by a severe ...

  20. Inference and the introductory statistics course

    NASA Astrophysics Data System (ADS)

    Pfannkuch, Maxine; Regan, Matt; Wild, Chris; Budgett, Stephanie; Forbes, Sharleen; Harraway, John; Parsonage, Ross

    2011-10-01

    This article sets out some of the rationale and arguments for making major changes to the teaching and learning of statistical inference in introductory courses at our universities by changing from a norm-based, mathematical approach to more conceptually accessible computer-based approaches. The core problem of the inferential argument with its hypothetical probabilistic reasoning process is examined in some depth. We argue that the revolution in the teaching of inference must begin. We also discuss some perplexing issues, problematic areas and some new insights into language conundrums associated with introducing the logic of inference through randomization methods.

  1. [Physiopathology of iodine deficiency].

    PubMed

    Pinchera, A; Rago, T; Vitti, P

    1998-01-01

    The process of goitrogenesis is likely to be the consequence of an increased TSH stimulation linked to an initial reduction of circulating thyroid hormone caused by iodine deficiency (ID). Other growth factors associated to TSH may have a role in the pathogenesis of goiter. Natural history of goiter is the evolution towards nodularity and functional autonomy. This phenomenon is due to the heterogeneity of thyroid follicular cells, some of which, with an intrinsic elevated growth rate, under the stimulation of ID progress to nodule formation and hyperfunction. In multinodular goiter TSH receptor mutations activating adenylate cyclase-cAMP pathway were found. In a recent epidemiological survey it was shown that nodular goiter increased with the age, being about 1% in schoolchildren and 23% in the adults (56-75 years). Also nodular autonomy and hyperthyroidism were more frequent in the 36-75 year age group. Severe ID is also cause of endemic cretinism. In Europe minor neuropsychological impairments and cognitive deficits were described in areas of moderate ID. The exposure to a mild ID during fetal life causes minor neuropsychological damage. In conclusion, ID is responsible of goiter and its evolution towards nodularity and functional autonomy. Severe ID is also cause of endemic cretinism, while cognitive deficits and minor neuropsychological impairments were found in mild to moderate ID. PMID:10052165

  2. Iodine deficiency disorders.

    PubMed

    Elliott, T C

    1987-01-01

    Iodine deficiency disorder (IDD) affects 800 million people in the world, yet iodine supplementation is one of the most cost-effective nutritional interventions known. Iodine is incorporated into thyroid hormones, necessary for regulating metabolic rate, growth, and development of the brain and nervous system. IDD may appear as goiter in adults, usually not a serious problem, or in cretinism in children, which is marked by severe mental and physical retardation, with irreversible hearing and speech defects and either deaf-mutism, squint and paralysis, or stunting and edema. Children supplemented by age 1 or 2 can sometimes be helped. Foods contain variable amounts of iodine dependent on the soil where they are grown, hence mountainous and some inland regions have high goiter and IDD incidence. There are also goitrogenic foods, typically those of the cabbage family. Diagnosis is clinical or by blood tests for thyroid hormone levels and ratios. Finger-stick methods are available. Prevention of IDD is simple with either iodized salt or flour, iodinated central water supplies, injectable or oral iodine-containing oil. All cost about $.04 per person per year, except injections, which cost about $1 per person, but have the advantage that they could be combined with immunizations. Local problems with supplements are loss of iodine in salt with storage in tropics, and local production of cheaper uniodinated salt. Emphasis should be given to pregnant women and young children. There is no harm in giving pregnant women iodine injections in 2nd or 3rd trimester. PMID:12343033

  3. α1-Antitrypsin deficiency.

    PubMed

    Greene, Catherine M; Marciniak, Stefan J; Teckman, Jeffrey; Ferrarotti, Ilaria; Brantly, Mark L; Lomas, David A; Stoller, James K; McElvaney, Noel G

    2016-01-01

    α1-Antitrypsin deficiency (A1ATD) is an inherited disorder caused by mutations in SERPINA1, leading to liver and lung disease. It is not a rare disorder but frequently goes underdiagnosed or misdiagnosed as asthma, chronic obstructive pulmonary disease (COPD) or cryptogenic liver disease. The most frequent disease-associated mutations include the S allele and the Z allele of SERPINA1, which lead to the accumulation of misfolded α1-antitrypsin in hepatocytes, endoplasmic reticulum stress, low circulating levels of α1-antitrypsin and liver disease. Currently, there is no cure for severe liver disease and the only management option is liver transplantation when liver failure is life-threatening. A1ATD-associated lung disease predominately occurs in adults and is caused principally by inadequate protease inhibition. Treatment of A1ATD-associated lung disease includes standard therapies that are also used for the treatment of COPD, in addition to the use of augmentation therapy (that is, infusions of human plasma-derived, purified α1-antitrypsin). New therapies that target the misfolded α1-antitrypsin or attempt to correct the underlying genetic mutation are currently under development. PMID:27465791

  4. Betaine Deficiency in Maize 1

    PubMed Central

    Lerma, Claudia; Rich, Patrick J.; Ju, Grace C.; Yang, Wen-Ju; Hanson, Andrew D.; Rhodes, David

    1991-01-01

    Maize (Zea mays L.) is a betaine-accumulating species, but certain maize genotypes lack betaine almost completely; a single recessive gene has been implicated as the cause of this deficiency (D Rhodes, PJ Rich [1988] Plant Physiol 88: 102-108). This study was undertaken to determine whether betaine deficiency in diverse maize germplasm is conditioned by the same genetic locus, and to define the biochemical lesion(s) involved. Complementation tests indicated that all 13 deficient genotypes tested shared a common locus. One maize population (P77) was found to be segregating for betaine deficiency, and true breeding individuals were used to produce related lines with and without betaine. Leaf tissue of both betaine-positive and betaine-deficient lines readily converted supplied betaine aldehyde to betaine, but only the betaine-containing line was able to oxidize supplied choline to betaine. This locates the lesion in betaine-deficient plants at the choline → betaine aldehyde step of betaine synthesis. Consistent with this location, betaine-deficient plants were shown to have no detectable endogenous pool of betaine aldehyde. PMID:16668098

  5. Degradation monitoring using probabilistic inference

    NASA Astrophysics Data System (ADS)

    Alpay, Bulent

    In order to increase safety and improve economy and performance in a nuclear power plant (NPP), the source and extent of component degradations should be identified before failures and breakdowns occur. It is also crucial for the next generation of NPPs, which are designed to have a long core life and high fuel burnup to have a degradation monitoring system in order to keep the reactor in a safe state, to meet the designed reactor core lifetime and to optimize the scheduled maintenance. Model-based methods are based on determining the inconsistencies between the actual and expected behavior of the plant, and use these inconsistencies for detection and diagnostics of degradations. By defining degradation as a random abrupt change from the nominal to a constant degraded state of a component, we employed nonlinear filtering techniques based on state/parameter estimation. We utilized a Bayesian recursive estimation formulation in the sequential probabilistic inference framework and constructed a hidden Markov model to represent a general physical system. By addressing the problem of a filter's inability to estimate an abrupt change, which is called the oblivious filter problem in nonlinear extensions of Kalman filtering, and the sample impoverishment problem in particle filtering, we developed techniques to modify filtering algorithms by utilizing additional data sources to improve the filter's response to this problem. We utilized a reliability degradation database that can be constructed from plant specific operational experience and test and maintenance reports to generate proposal densities for probable degradation modes. These are used in a multiple hypothesis testing algorithm. We then test samples drawn from these proposal densities with the particle filtering estimates based on the Bayesian recursive estimation formulation with the Metropolis Hastings algorithm, which is a well-known Markov chain Monte Carlo method (MCMC). This multiple hypothesis testing

  6. "Myelodysplasia," myeloneuropathy, and copper deficiency.

    PubMed

    Kumar, Neeraj; Elliott, Michelle A; Hoyer, James D; Harper, Charles M; Ahlskog, J Eric; Phyliky, Robert L

    2005-07-01

    We describe a patient with a suspected myelodysplastic syndrome that developed in association with a neurologic disorder resembling subacute combined degeneration but without vitamin B12 deficiency. Ultimately, the hematologic manifestations and the neurologic syndrome were linked to severe copper deficiency. Prompt and complete reversal of the hematologic abnormalities occurred with copper replacement. Serum copper determination should be included in the work-up of patients with anemia and leukopenia of unclear etiology who have associated myeloneuropathy. The hematologic picture can resemble sideroblastic anemia or myelodysplastic syndrome. Hyperzincemia can be an accompanying abnormality even without exogenous zinc ingestion. The reason for the copper deficiency may not be evident. PMID:16007901

  7. Clinical manifestations of zinc deficiency.

    PubMed

    Prasad, A S

    1985-01-01

    The essentiality of zinc for humans was recognized in the early 1960s. The causes of zinc deficiency include malnutrition, alcoholism, malabsorption, extensive burns, chronic debilitating disorders, chronic renal diseases, following uses of certain drugs such as penicillamine for Wilson's disease and diuretics in some cases, and genetic disorders such as acrodermatitis enteropathica and sickle cell disease. In pregnancy and during periods of growth the requirement of zinc is increased. The clinical manifestations in severe cases of zinc deficiency include bullous-pustular dermatitis, alopecia, diarrhea, emotional disorder, weight loss, intercurrent infections, hypogonadism in males; it is fatal if unrecognized and untreated. A moderate deficiency of zinc is characterized by growth retardation and delayed puberty in adolescents, hypogonadism in males, rough skin, poor appetite, mental lethargy, delayed wound healing, taste abnormalities, and abnormal dark adaptation. In mild cases of zinc deficiency in human subjects, we have observed oligospermia, slight weight loss, and hyperammonemia. Zinc is a growth factor. Its deficiency adversely affects growth in many animal species and humans. Inasmuch as zinc is needed for protein and DNA synthesis and for cell division, it is believed that the growth effect of zinc is related to its effect on protein synthesis. Whether or not zinc is required for the metabolism of somatomedin needs to be investigated in the future. Testicular functions are affected adversely as a result of zinc deficiency in both humans and experimental animals. This effect of zinc is at the end organ level; the hypothalamic-pituitary axis is intact in zinc-deficient subjects. Inasmuch as zinc is intimately involved in cell division, its deficiency may adversely affect testicular size and thus affect its functions. Zinc is required for the functions of several enzymes and whether or not it has an enzymatic role in steroidogenesis is not known at present

  8. Genetics of growth hormone deficiency.

    PubMed

    Mullis, Primus E

    2007-03-01

    When a child is not following the normal, predicted growth curve, an evaluation for underlying illness and central nervous system abnormalities is required and appropriate consideration should be given to genetic defects causing growth hormone (GH) deficiency. This article focuses on the GH gene, the various gene alterations, and their possible impact on the pituitary gland. Transcription factors regulating pituitary gland development may cause multiple pituitary hormone deficiency but may present initially as GH deficiency. The role of two most important transcription factors, POU1F1 (Pit-1) and PROP 1, is discussed. PMID:17336732

  9. [Immune deficiencies in nutritional anemias].

    PubMed

    Bonnet Gajdos, M; Navarro, J; Belas, F; Traineau, R

    1982-12-16

    A transient cellular immunologic defect caused by folic acid deficiency was seen in a goat-milk-fed infant with severe enterocolitis. Data on the immunologic consequences of folic acid, protein and iron deficiencies were reviewed in the medical literature. Investigations are difficult because of the patients' poor general condition. Results are difficult to interpret as many etiologic factors are often combined and mechanisms of immunologic responses are complex. Attention is drawn to the danger of iron therapy in patients with transferrin deficiency. PMID:6297076

  10. An inference engine for embedded diagnostic systems

    NASA Technical Reports Server (NTRS)

    Fox, Barry R.; Brewster, Larry T.

    1987-01-01

    The implementation of an inference engine for embedded diagnostic systems is described. The system consists of two distinct parts. The first is an off-line compiler which accepts a propositional logical statement of the relationship between facts and conclusions and produces data structures required by the on-line inference engine. The second part consists of the inference engine and interface routines which accept assertions of fact and return the conclusions which necessarily follow. Given a set of assertions, it will generate exactly the conclusions which logically follow. At the same time, it will detect any inconsistencies which may propagate from an inconsistent set of assertions or a poorly formulated set of rules. The memory requirements are fixed and the worst case execution times are bounded at compile time. The data structures and inference algorithms are very simple and well understood. The data structures and algorithms are described in detail. The system has been implemented on Lisp, Pascal, and Modula-2.

  11. Metamodel-Driven Evolution with Grammar Inference

    NASA Astrophysics Data System (ADS)

    Bryant, Barrett R.; Liu, Qichao; Mernik, Marjan

    2010-10-01

    Domain-specific modeling (DSM) has become one of the most popular techniques for incorporating model-driven engineering (MDE) into software engineering. In DSM, domain experts define metamodels to describe the essential problems in a domain. A model conforms to a schema definition represented by a metamodel in a similar manner to a programming language conforms to a grammar. Metamodel-driven evolution is when a metamodel undergoes evolutions to incorporate new concerns in the domain. However, this results in losing the ability to use existing model instances. Grammar inference is the problem of inferring a grammar from sample strings which the grammar should generate. This paper describes our work in solving the problem of metamodel-driven evolution with grammar inference, by inferring the metamodel from model instances.

  12. Critical Thinking: Distinguishing between Inferences and Assumptions.

    ERIC Educational Resources Information Center

    Elder, Linda; Paul, Richard

    2002-01-01

    Outlines the differences between inferences and assumptions in critical thinking processes. Explains that as students develop critical intuitions, they increasingly notice how their point of view shapes their experiences. (AUTH/NB)

  13. Are Evaluations Inferred Directly From Overt Actions?

    ERIC Educational Resources Information Center

    Brown, Donald; And Others

    1975-01-01

    The operation of a covert information processing mechanism was investigated in two experiments of the self-persuasion phenomena; i. e., making an inference about a stimulus on the basis of one's past behavior. (Editor)

  14. Multisensory causal inference in the brain.

    PubMed

    Kayser, Christoph; Shams, Ladan

    2015-02-01

    At any given moment, our brain processes multiple inputs from its different sensory modalities (vision, hearing, touch, etc.). In deciphering this array of sensory information, the brain has to solve two problems: (1) which of the inputs originate from the same object and should be integrated and (2) for the sensations originating from the same object, how best to integrate them. Recent behavioural studies suggest that the human brain solves these problems using optimal probabilistic inference, known as Bayesian causal inference. However, how and where the underlying computations are carried out in the brain have remained unknown. By combining neuroimaging-based decoding techniques and computational modelling of behavioural data, a new study now sheds light on how multisensory causal inference maps onto specific brain areas. The results suggest that the complexity of neural computations increases along the visual hierarchy and link specific components of the causal inference process with specific visual and parietal regions. PMID:25710476

  15. Probabilistic inferences related to the measurement process

    NASA Astrophysics Data System (ADS)

    Rossi, G. B.

    2010-07-01

    In measurement indications from a measuring system are acquired and, on the basis of them, some inference about the measurand is made. The final result may be the assignment of a probability distribution for the possible values of the measurand. We discuss the logical structure of such an inference and some of its epistemological consequences. In particular, we propose a new solution to the problem of systematic effects in measurement.

  16. Causal inference in economics and marketing.

    PubMed

    Varian, Hal R

    2016-07-01

    This is an elementary introduction to causal inference in economics written for readers familiar with machine learning methods. The critical step in any causal analysis is estimating the counterfactual-a prediction of what would have happened in the absence of the treatment. The powerful techniques used in machine learning may be useful for developing better estimates of the counterfactual, potentially improving causal inference. PMID:27382144

  17. Symbolic transfer entropy: inferring directionality in biosignals.

    PubMed

    Staniek, Matthäus; Lehnertz, Klaus

    2009-12-01

    Inferring directional interactions from biosignals is of crucial importance to improve understanding of dynamical interdependences underlying various physiological and pathophysiological conditions. We here present symbolic transfer entropy as a robust measure to infer the direction of interactions between multidimensional dynamical systems. We demonstrate its performance in quantifying driver-responder relationships in a network of coupled nonlinear oscillators and in the human epileptic brain. PMID:19938889

  18. Causal inference in economics and marketing

    PubMed Central

    Varian, Hal R.

    2016-01-01

    This is an elementary introduction to causal inference in economics written for readers familiar with machine learning methods. The critical step in any causal analysis is estimating the counterfactual—a prediction of what would have happened in the absence of the treatment. The powerful techniques used in machine learning may be useful for developing better estimates of the counterfactual, potentially improving causal inference. PMID:27382144

  19. Operation of the Bayes Inference Engine

    SciTech Connect

    Hanson, K.M.; Cunningham, G.S.

    1998-07-27

    The authors have developed a computer application, called the Bayes Inference Engine, to enable one to make inferences about models of a physical object from radiographs taken of it. In the BIE calculational models are represented by a data-flow diagram that can be manipulated by the analyst in a graphical-programming environment. The authors demonstrate the operation of the BIE in terms of examples of two-dimensional tomographic reconstruction including uncertainty estimation.

  20. Genetics Home Reference: tetrahydrobiopterin deficiency

    MedlinePlus

    ... 3. Citation on PubMed Liu TT, Chiang SH, Wu SJ, Hsiao KJ. Tetrahydrobiopterin-deficient hyperphenylalaninemia in the ... Citation on PubMed Wang L, Yu WM, He C, Chang M, Shen M, Zhou Z, Zhang Z, ...

  1. Genetics Home Reference: arginase deficiency

    MedlinePlus

    ... deficiency is an inherited disorder that causes the amino acid arginine (a building block of proteins) and ammonia ... links) Encyclopedia: Hereditary urea cycle abnormality Health Topic: Amino Acid Metabolism Disorders Health Topic: Genetic Brain Disorders Health ...

  2. Genetics Home Reference: prekallikrein deficiency

    MedlinePlus

    ... a role in a process called the intrinsic coagulation pathway (also called the contact activation pathway). This ... functional plasma kallikrein, which likely impairs the intrinsic coagulation pathway. Researchers suggest that this lack (deficiency) of ...

  3. Genetics Home Reference: dihydropyrimidinase deficiency

    MedlinePlus

    ... An abnormally small head size ( microcephaly ) and autistic behaviors that affect communication and social interaction also occur ... deficiency MalaCards: dihydropyrimidinuria Merck Manual Professional Version: Pyrimidine ... Dihydropyrimidinuria Patient Support and Advocacy Resources ( ...

  4. Evolutionary Processes and Mental Deficiency

    ERIC Educational Resources Information Center

    Spitz, Herman H.

    1973-01-01

    The author hypothesizes that central nervous system damage of deficiency associated with mental retardation affects primarily those cortical processes which developed at a late stage in man's evolutionary history. (Author)

  5. [Niacin deficiency and cutaneous immunity].

    PubMed

    Ikenouchi-Sugita, Atsuko; Sugita, Kazunari

    2015-01-01

    Niacin, also known as vitamin B3, is required for the synthesis of coenzymes, nicotinamide adenine dinucleotide (NAD) and nicotinamide adenine dinucleotide phosphate (NADP). Niacin binds with G protein-coupled receptor (GPR) 109A on cutaneous Langerhans cells and causes vasodilation with flushing in head and neck area. Niacin deficiency due to excessive alcohol consumption, certain drugs or inadequate uptake in diet causes pellagra, a photosensitivity dermatitis. Recently several studies have revealed the mechanism of photosensitivity in niacin deficiency, which may pave a way for new therapeutic approaches. The expression level of prostaglandin E synthase (PTGES) is up-regulated in the skin of both pellagra patients and niacin deficient pellagra mouse models. In addition, pellagra is mediated through prostaglandin E₂-EP4 (PGE₂-EP4) signaling via reactive oxygen species (ROS) production in keratinocytes. In this article, we have reviewed the role of niacin in immunity and the mechanism of niacin deficiency-induced photosensitivity. PMID:25765687

  6. Detecting Alpha-1 Antitrypsin Deficiency.

    PubMed

    Stoller, James K

    2016-08-01

    Alpha-1 antitrypsin deficiency is a widely underrecognized condition, with evidence of persisting long diagnostic delays and patients' frequent need to see multiple physicians before initial diagnosis. Reasons for underrecognition include inadequate understanding of alpha-1 antitrypsin deficiency by physicians and allied health care providers; failure to implement available, guideline-based practice recommendations; and the belief that effective therapy is unavailable. Multiple studies have described both the results of screening and targeted detection of individuals with alpha-1 antitrypsin deficiency, with both varying strategies employed to identify at-risk individuals and varying results of testing. Also, various strategies to enhance detection of affected individuals have been examined, including use of the electronic medical record to prompt testing and empowerment of allied health providers, especially respiratory therapists, to promote testing for alpha-1 antitrypsin deficiency. Such efforts are likely to enhance detection with the expected result that the harmful effects of delayed diagnosis can be mitigated. PMID:27564667

  7. Genetics Home Reference: prothrombin deficiency

    MedlinePlus

    ... Patients and Caregivers: How Blood Clots Orphanet: Congenital factor II deficiency University of Iowa Health Care: Prothrombin Gene Mutation Patient Support and Advocacy Resources (2 links) Canadian Hemophilia Society National Hemophilia Foundation: Factor II ... Genetic Testing Registry (1 link) Prothrombin ...

  8. Cutaneous findings of nutritional deficiencies in children.

    PubMed

    Goskowicz, M; Eichenfield, L F

    1993-08-01

    Nutritional deficiencies may be associated with a variety of cutaneous findings in children. This review emphasizes new developments relating to cutaneous findings of nutritional deficiencies. Zinc deficiency, acrodermatitis enteropathica, and acrodermatitis enteropathica-like eruptions are seen with a variety of conditions including cystic fibrosis, anorexia nervosa, and breastfeeding. Similar cutaneous findings not related to zinc deficiency may also occur with such metabolic disorders as methylmalonic aciduria, multiple carboxylase deficiency, essential fatty acid deficiency and other amino acid deficiencies. Vitamin K deficiency is associated with hemorrhagic disease of the newborn and coagulopathy. Vitamin A deficiency presents with a variety of systemic findings and distinctive dermatologic findings. Acute vitamin A deficiency may be seen in children infected with measles and is associated with more severe disease. The systemic and cutaneous findings of vitamin C deficiency, scurvy, are discussed. PMID:8374671

  9. On the criticality of inferred models

    NASA Astrophysics Data System (ADS)

    Mastromatteo, Iacopo; Marsili, Matteo

    2011-10-01

    Advanced inference techniques allow one to reconstruct a pattern of interaction from high dimensional data sets, from probing simultaneously thousands of units of extended systems—such as cells, neural tissues and financial markets. We focus here on the statistical properties of inferred models and argue that inference procedures are likely to yield models which are close to singular values of parameters, akin to critical points in physics where phase transitions occur. These are points where the response of physical systems to external perturbations, as measured by the susceptibility, is very large and diverges in the limit of infinite size. We show that the reparameterization invariant metrics in the space of probability distributions of these models (the Fisher information) are directly related to the susceptibility of the inferred model. As a result, distinguishable models tend to accumulate close to critical points, where the susceptibility diverges in infinite systems. This region is the one where the estimate of inferred parameters is most stable. In order to illustrate these points, we discuss inference of interacting point processes with application to financial data and show that sensible choices of observation time scales naturally yield models which are close to criticality.

  10. Zinc and its deficiency diseases.

    PubMed

    Evans, G W

    1986-01-01

    The pervasive role of zinc in the metabolic function of the body results from its function as a cofactor of a multitude of enzymes. Zinc is found in every tissue in the body, and because zinc metalloenzymes are found in every known class of enzymes, the metal has a function in every conceivable type of biochemical pathway. Symptoms resulting from zinc deficiency are as diverse as the enzymes with which the metal is associated. If chronic, severe, and untreated, zinc deficiency can be fatal. Less drastic symptoms include infections, hypogonadism, weight loss, emotional disturbance, dermatitis, alopecia, impaired taste acuity, night blindness, poor appetite, delayed wound healing, and elevated blood ammonia levels. Many symptoms of zinc deficiency result from poor diet consumption, but often the most severe symptoms result from other factors including excessive alcohol use, liver diseases, malabsorption syndromes, renal disease, enteral or parenteral alimentation, administration of sulfhydryl-containing drugs, and sickle cell disease. The most severe symptoms of zinc deficiency occur in young children affected with the autosomal-recessive trait, acrodermatitis enteropathica. This disease results in decreased synthesis of picolinic acid which causes an impaired ability to utilize zinc from common food. Because simple laboratory analyses are often not reliable in determining zinc nutriture of a patient, those symptoms caused by suspected zinc deficiency are best verified by the oral administration of zinc dipicolinate. This zinc compound is efficacious and safe and would provide an accurate means of identifying symptoms that do result from zinc deficiency. PMID:3514057

  11. 33 CFR 154.1070 - Deficiencies.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... equipment or records maintained in connection with this subpart. (b) Deficiencies shall be corrected within... who disagrees with a deficiency issued by the COTP may appeal the deficiency to the cognizant COTP within 7 days or the time specified by the COTP to correct the deficiency, whichever is less. This...

  12. Inference of Isoforms from Short Sequence Reads

    NASA Astrophysics Data System (ADS)

    Feng, Jianxing; Li, Wei; Jiang, Tao

    Due to alternative splicing events in eukaryotic species, the identification of mRNA isoforms (or splicing variants) is a difficult problem. Traditional experimental methods for this purpose are time consuming and cost ineffective. The emerging RNA-Seq technology provides a possible effective method to address this problem. Although the advantages of RNA-Seq over traditional methods in transcriptome analysis have been confirmed by many studies, the inference of isoforms from millions of short sequence reads (e.g., Illumina/Solexa reads) has remained computationally challenging. In this work, we propose a method to calculate the expression levels of isoforms and infer isoforms from short RNA-Seq reads using exon-intron boundary, transcription start site (TSS) and poly-A site (PAS) information. We first formulate the relationship among exons, isoforms, and single-end reads as a convex quadratic program, and then use an efficient algorithm (called IsoInfer) to search for isoforms. IsoInfer can calculate the expression levels of isoforms accurately if all the isoforms are known and infer novel isoforms from scratch. Our experimental tests on known mouse isoforms with both simulated expression levels and reads demonstrate that IsoInfer is able to calculate the expression levels of isoforms with an accuracy comparable to the state-of-the-art statistical method and a 60 times faster speed. Moreover, our tests on both simulated and real reads show that it achieves a good precision and sensitivity in inferring isoforms when given accurate exon-intron boundary, TSS and PAS information, especially for isoforms whose expression levels are significantly high.

  13. Mental state inference using visual control parameters.

    PubMed

    Oztop, Erhan; Wolpert, Daniel; Kawato, Mitsuo

    2005-02-01

    Although we can often infer the mental states of others by observing their actions, there are currently no computational models of this remarkable ability. Here we develop a computational model of mental state inference that builds upon a generic visuomanual feedback controller, and implements mental simulation and mental state inference functions using circuitry that subserves sensorimotor control. Our goal is (1) to show that control mechanisms developed for manual manipulation are readily endowed with visual and predictive processing capabilities and thus allows a natural extension to the understanding of movements performed by others; and (2) to give an explanation on how cortical regions, in particular the parietal and premotor cortices, may be involved in such dual mechanism. To analyze the model, we simulate tasks in which an observer watches an actor performing either a reaching or a grasping movement. The observer's goal is to estimate the 'mental state' of the actor: the goal of the reaching movement or the intention of the agent performing the grasping movement. We show that the motor modules of the observer can be used in a 'simulation mode' to infer the mental state of the actor. The simulations with different grasping and non-straight line reaching strategies show that the mental state inference model is applicable to complex movements. Moreover, we simulate deceptive reaching, where an actor imposes false beliefs about his own mental state on an observer. The simulations show that computational elements developed for sensorimotor control are effective in inferring the mental states of others. The parallels between the model and cortical organization of movement suggest that primates might have developed a similar resource utilization strategy for action understanding, and thus lead to testable predictions about the brain mechanisms of mental state inference. PMID:15653289

  14. Inference of complex biological networks: distinguishability issues and optimization-based solutions

    PubMed Central

    2011-01-01

    Background The inference of biological networks from high-throughput data has received huge attention during the last decade and can be considered an important problem class in systems biology. However, it has been recognized that reliable network inference remains an unsolved problem. Most authors have identified lack of data and deficiencies in the inference algorithms as the main reasons for this situation. Results We claim that another major difficulty for solving these inference problems is the frequent lack of uniqueness of many of these networks, especially when prior assumptions have not been taken properly into account. Our contributions aid the distinguishability analysis of chemical reaction network (CRN) models with mass action dynamics. The novel methods are based on linear programming (LP), therefore they allow the efficient analysis of CRNs containing several hundred complexes and reactions. Using these new tools and also previously published ones to obtain the network structure of biological systems from the literature, we find that, often, a unique topology cannot be determined, even if the structure of the corresponding mathematical model is assumed to be known and all dynamical variables are measurable. In other words, certain mechanisms may remain undetected (or they are falsely detected) while the inferred model is fully consistent with the measured data. It is also shown that sparsity enforcing approaches for determining 'true' reaction structures are generally not enough without additional prior information. Conclusions The inference of biological networks can be an extremely challenging problem even in the utopian case of perfect experimental information. Unfortunately, the practical situation is often more complex than that, since the measurements are typically incomplete, noisy and sometimes dynamically not rich enough, introducing further obstacles to the structure/parameter estimation process. In this paper, we show how the structural

  15. Estimating uncertainty of inference for validation

    SciTech Connect

    Booker, Jane M; Langenbrunner, James R; Hemez, Francois M; Ross, Timothy J

    2010-09-30

    We present a validation process based upon the concept that validation is an inference-making activity. This has always been true, but the association has not been as important before as it is now. Previously, theory had been confirmed by more data, and predictions were possible based on data. The process today is to infer from theory to code and from code to prediction, making the role of prediction somewhat automatic, and a machine function. Validation is defined as determining the degree to which a model and code is an accurate representation of experimental test data. Imbedded in validation is the intention to use the computer code to predict. To predict is to accept the conclusion that an observable final state will manifest; therefore, prediction is an inference whose goodness relies on the validity of the code. Quantifying the uncertainty of a prediction amounts to quantifying the uncertainty of validation, and this involves the characterization of uncertainties inherent in theory/models/codes and the corresponding data. An introduction to inference making and its associated uncertainty is provided as a foundation for the validation problem. A mathematical construction for estimating the uncertainty in the validation inference is then presented, including a possibility distribution constructed to represent the inference uncertainty for validation under uncertainty. The estimation of inference uncertainty for validation is illustrated using data and calculations from Inertial Confinement Fusion (ICF). The ICF measurements of neutron yield and ion temperature were obtained for direct-drive inertial fusion capsules at the Omega laser facility. The glass capsules, containing the fusion gas, were systematically selected with the intent of establishing a reproducible baseline of high-yield 10{sup 13}-10{sup 14} neutron output. The deuterium-tritium ratio in these experiments was varied to study its influence upon yield. This paper on validation inference is the

  16. Deep Learning for Population Genetic Inference

    PubMed Central

    Sheehan, Sara; Song, Yun S.

    2016-01-01

    Given genomic variation data from multiple individuals, computing the likelihood of complex population genetic models is often infeasible. To circumvent this problem, we introduce a novel likelihood-free inference framework by applying deep learning, a powerful modern technique in machine learning. Deep learning makes use of multilayer neural networks to learn a feature-based function from the input (e.g., hundreds of correlated summary statistics of data) to the output (e.g., population genetic parameters of interest). We demonstrate that deep learning can be effectively employed for population genetic inference and learning informative features of data. As a concrete application, we focus on the challenging problem of jointly inferring natural selection and demography (in the form of a population size change history). Our method is able to separate the global nature of demography from the local nature of selection, without sequential steps for these two factors. Studying demography and selection jointly is motivated by Drosophila, where pervasive selection confounds demographic analysis. We apply our method to 197 African Drosophila melanogaster genomes from Zambia to infer both their overall demography, and regions of their genome under selection. We find many regions of the genome that have experienced hard sweeps, and fewer under selection on standing variation (soft sweep) or balancing selection. Interestingly, we find that soft sweeps and balancing selection occur more frequently closer to the centromere of each chromosome. In addition, our demographic inference suggests that previously estimated bottlenecks for African Drosophila melanogaster are too extreme. PMID:27018908

  17. Scene Construction, Visual Foraging, and Active Inference

    PubMed Central

    Mirza, M. Berk; Adams, Rick A.; Mathys, Christoph D.; Friston, Karl J.

    2016-01-01

    This paper describes an active inference scheme for visual searches and the perceptual synthesis entailed by scene construction. Active inference assumes that perception and action minimize variational free energy, where actions are selected to minimize the free energy expected in the future. This assumption generalizes risk-sensitive control and expected utility theory to include epistemic value; namely, the value (or salience) of information inherent in resolving uncertainty about the causes of ambiguous cues or outcomes. Here, we apply active inference to saccadic searches of a visual scene. We consider the (difficult) problem of categorizing a scene, based on the spatial relationship among visual objects where, crucially, visual cues are sampled myopically through a sequence of saccadic eye movements. This means that evidence for competing hypotheses about the scene has to be accumulated sequentially, calling upon both prediction (planning) and postdiction (memory). Our aim is to highlight some simple but fundamental aspects of the requisite functional anatomy; namely, the link between approximate Bayesian inference under mean field assumptions and functional segregation in the visual cortex. This link rests upon the (neurobiologically plausible) process theory that accompanies the normative formulation of active inference for Markov decision processes. In future work, we hope to use this scheme to model empirical saccadic searches and identify the prior beliefs that underwrite intersubject variability in the way people forage for information in visual scenes (e.g., in schizophrenia). PMID:27378899

  18. Scene Construction, Visual Foraging, and Active Inference.

    PubMed

    Mirza, M Berk; Adams, Rick A; Mathys, Christoph D; Friston, Karl J

    2016-01-01

    This paper describes an active inference scheme for visual searches and the perceptual synthesis entailed by scene construction. Active inference assumes that perception and action minimize variational free energy, where actions are selected to minimize the free energy expected in the future. This assumption generalizes risk-sensitive control and expected utility theory to include epistemic value; namely, the value (or salience) of information inherent in resolving uncertainty about the causes of ambiguous cues or outcomes. Here, we apply active inference to saccadic searches of a visual scene. We consider the (difficult) problem of categorizing a scene, based on the spatial relationship among visual objects where, crucially, visual cues are sampled myopically through a sequence of saccadic eye movements. This means that evidence for competing hypotheses about the scene has to be accumulated sequentially, calling upon both prediction (planning) and postdiction (memory). Our aim is to highlight some simple but fundamental aspects of the requisite functional anatomy; namely, the link between approximate Bayesian inference under mean field assumptions and functional segregation in the visual cortex. This link rests upon the (neurobiologically plausible) process theory that accompanies the normative formulation of active inference for Markov decision processes. In future work, we hope to use this scheme to model empirical saccadic searches and identify the prior beliefs that underwrite intersubject variability in the way people forage for information in visual scenes (e.g., in schizophrenia). PMID:27378899

  19. Computationally efficient Bayesian inference for inverse problems.

    SciTech Connect

    Marzouk, Youssef M.; Najm, Habib N.; Rahn, Larry A.

    2007-10-01

    Bayesian statistics provides a foundation for inference from noisy and incomplete data, a natural mechanism for regularization in the form of prior information, and a quantitative assessment of uncertainty in the inferred results. Inverse problems - representing indirect estimation of model parameters, inputs, or structural components - can be fruitfully cast in this framework. Complex and computationally intensive forward models arising in physical applications, however, can render a Bayesian approach prohibitive. This difficulty is compounded by high-dimensional model spaces, as when the unknown is a spatiotemporal field. We present new algorithmic developments for Bayesian inference in this context, showing strong connections with the forward propagation of uncertainty. In particular, we introduce a stochastic spectral formulation that dramatically accelerates the Bayesian solution of inverse problems via rapid evaluation of a surrogate posterior. We also explore dimensionality reduction for the inference of spatiotemporal fields, using truncated spectral representations of Gaussian process priors. These new approaches are demonstrated on scalar transport problems arising in contaminant source inversion and in the inference of inhomogeneous material or transport properties. We also present a Bayesian framework for parameter estimation in stochastic models, where intrinsic stochasticity may be intermingled with observational noise. Evaluation of a likelihood function may not be analytically tractable in these cases, and thus several alternative Markov chain Monte Carlo (MCMC) schemes, operating on the product space of the observations and the parameters, are introduced.

  20. Deep Learning for Population Genetic Inference.

    PubMed

    Sheehan, Sara; Song, Yun S

    2016-03-01

    Given genomic variation data from multiple individuals, computing the likelihood of complex population genetic models is often infeasible. To circumvent this problem, we introduce a novel likelihood-free inference framework by applying deep learning, a powerful modern technique in machine learning. Deep learning makes use of multilayer neural networks to learn a feature-based function from the input (e.g., hundreds of correlated summary statistics of data) to the output (e.g., population genetic parameters of interest). We demonstrate that deep learning can be effectively employed for population genetic inference and learning informative features of data. As a concrete application, we focus on the challenging problem of jointly inferring natural selection and demography (in the form of a population size change history). Our method is able to separate the global nature of demography from the local nature of selection, without sequential steps for these two factors. Studying demography and selection jointly is motivated by Drosophila, where pervasive selection confounds demographic analysis. We apply our method to 197 African Drosophila melanogaster genomes from Zambia to infer both their overall demography, and regions of their genome under selection. We find many regions of the genome that have experienced hard sweeps, and fewer under selection on standing variation (soft sweep) or balancing selection. Interestingly, we find that soft sweeps and balancing selection occur more frequently closer to the centromere of each chromosome. In addition, our demographic inference suggests that previously estimated bottlenecks for African Drosophila melanogaster are too extreme. PMID:27018908

  1. Hierarchical cosmic shear power spectrum inference

    NASA Astrophysics Data System (ADS)

    Alsing, Justin; Heavens, Alan; Jaffe, Andrew H.; Kiessling, Alina; Wandelt, Benjamin; Hoffmann, Till

    2016-02-01

    We develop a Bayesian hierarchical modelling approach for cosmic shear power spectrum inference, jointly sampling from the posterior distribution of the cosmic shear field and its (tomographic) power spectra. Inference of the shear power spectrum is a powerful intermediate product for a cosmic shear analysis, since it requires very few model assumptions and can be used to perform inference on a wide range of cosmological models a posteriori without loss of information. We show that joint posterior for the shear map and power spectrum can be sampled effectively by Gibbs sampling, iteratively drawing samples from the map and power spectrum, each conditional on the other. This approach neatly circumvents difficulties associated with complicated survey geometry and masks that plague frequentist power spectrum estimators, since the power spectrum inference provides prior information about the field in masked regions at every sampling step. We demonstrate this approach for inference of tomographic shear E-mode, B-mode and EB-cross power spectra from a simulated galaxy shear catalogue with a number of important features; galaxies distributed on the sky and in redshift with photometric redshift uncertainties, realistic random ellipticity noise for every galaxy and a complicated survey mask. The obtained posterior distributions for the tomographic power spectrum coefficients recover the underlying simulated power spectra for both E- and B-modes.

  2. Inferring learners' knowledge from their actions.

    PubMed

    Rafferty, Anna N; LaMar, Michelle M; Griffiths, Thomas L

    2015-04-01

    Watching another person take actions to complete a goal and making inferences about that person's knowledge is a relatively natural task for people. This ability can be especially important in educational settings, where the inferences can be used for assessment, diagnosing misconceptions, and providing informative feedback. In this paper, we develop a general framework for automatically making such inferences based on observed actions; this framework is particularly relevant for inferring student knowledge in educational games and other interactive virtual environments. Our approach relies on modeling action planning: We formalize the problem as a Markov decision process in which one must choose what actions to take to complete a goal, where choices will be dependent on one's beliefs about how actions affect the environment. We use a variation of inverse reinforcement learning to infer these beliefs. Through two lab experiments, we show that this model can recover people's beliefs in a simple environment, with accuracy comparable to that of human observers. We then demonstrate that the model can be used to provide real-time feedback and to model data from an existing educational game. PMID:25155381

  3. Cluster Mass Inference via Random Field Theory

    PubMed Central

    Zhang, Hui; Nichols, Thomas E.; Johnson, Timothy D.

    2009-01-01

    Cluster extent and voxel intensity are two widely used statistics in neuroimaging inference. Cluster extent is sensitive to spatially extended signals while voxel intensity is better for intense but focal signals. In order to leverage strength from both statistics, several nonparametric permutation methods have been proposed to combine the two methods. Simulation studies have shown that of the different cluster permutation methods, the cluster mass statistic is generally the best. However, to date, there is no parametric cluster mass inference method available. In this paper, we propose a cluster mass inference method based on random field theory (RFT). We develop this method for Gaussian images, evaluate it on Gaussian and Gaussianized t-statistic images and investigate its statistical properties via simulation studies and real data. Simulation results show that the method is valid under the null hypothesis and demonstrate that it can be more powerful than the cluster extent inference method. Further, analyses with a single-subject and a group fMRI dataset demonstrate better power than traditional cluster extent inference, and good accuracy relative to a gold-standard permutation test. PMID:18805493

  4. Reliability of the Granger causality inference

    NASA Astrophysics Data System (ADS)

    Zhou, Douglas; Zhang, Yaoyu; Xiao, Yanyang; Cai, David

    2014-04-01

    How to characterize information flows in physical, biological, and social systems remains a major theoretical challenge. Granger causality (GC) analysis has been widely used to investigate information flow through causal interactions. We address one of the central questions in GC analysis, that is, the reliability of the GC evaluation and its implications for the causal structures extracted by this analysis. Our work reveals that the manner in which a continuous dynamical process is projected or coarse-grained to a discrete process has a profound impact on the reliability of the GC inference, and different sampling may potentially yield completely opposite inferences. This inference hazard is present for both linear and nonlinear processes. We emphasize that there is a hazard of reaching incorrect conclusions about network topologies, even including statistical (such as small-world or scale-free) properties of the networks, when GC analysis is blindly applied to infer the network topology. We demonstrate this using a small-world network for which a drastic loss of small-world attributes occurs in the reconstructed network using the standard GC approach. We further show how to resolve the paradox that the GC analysis seemingly becomes less reliable when more information is incorporated using finer and finer sampling. Finally, we present strategies to overcome these inference artifacts in order to obtain a reliable GC result.

  5. Health consequences of iodine deficiency.

    PubMed

    Kapil, Umesh

    2007-12-01

    Iodine Deficiency Disorders (IDD) are one of the biggest worldwide public health problem of today. Their effect is hidden and profoundly affects the quality of human life. Iodine deficiency occurs when the soil is poor in iodine, causing a low concentration in food products and insufficient iodine intake in the population. When iodine requirements are not met, the thyroid may no longer be able to synthesize sufficient amounts of thyroid hormone. The resulting low-level of thyroid hormones in the blood is the principal factor responsible for the series of functional and developmental abnormalities, collectively referred to as IDD. Iodine deficiency is a significant cause of mental developmental problems in children, including implications on reproductive functions and lowering of IQ levels in school-aged children. The consequence of iodine deficiency during pregnancy is impaired synthesis of thyroid hormones by the mother and the foetus. An insufficient supply of thyroid hormones to the developing brain may result in mental retardation. Brain damage and irreversible mental retardation are the most important disorders induced by iodine deficiency. Daily consumption of salt fortified with iodine is a proven effective strategy for prevention of IDD. PMID:21748117

  6. Zinc deficiency in elderly patients.

    PubMed

    Prasad, A S; Fitzgerald, J T; Hess, J W; Kaplan, J; Pelen, F; Dardenne, M

    1993-01-01

    Zinc is needed for growth and development, DNA synthesis, neurosensory functions, and cell-mediated immunity. Although zinc intake is reduced in elderly people, its deficiency and effects on cell-mediated immunity of the elderly have not been established. Subjects enrolled in "A Model Health Promotion and Intervention Program for Urban Middle Aged and Elderly Americans" were assessed for nutrition and zinc status. One hundred eighty healthy subjects were randomly selected for the study. Their mean dietary zinc intake was 9.06 mg/day, whereas the recommended dietary allowance is 15 mg/day. Plasma zinc was normal, but zinc in granulocytes and lymphocytes were decreased compared with younger control subjects. Of 118 elderly subjects in whom zinc levels in both granulocytes and lymphocytes were available, 36 had deficient levels. Plasma copper was increased, and interleukin 1 (IL-1) production was significantly decreased. Reduced response to the skin-test antigen panel and decreased taste acuity were observed. Thirteen elderly zinc-deficient subjects were supplemented with zinc, and various variables were assessed before and after zinc supplementation. Zinc supplementation corrected zinc deficiency and normalized plasma copper levels. Serum thymulin activity, IL-1 production, and lymphocyte ecto-5'-nucleotidase increased significantly after supplementation. Improvement in response to skin-test antigens and taste acuity was observed after zinc supplementation. A mild zinc deficiency appears to be a significant clinical problem in free-living elderly people. PMID:8353362

  7. Leaf Senescence by Magnesium Deficiency

    PubMed Central

    Tanoi, Keitaro; Kobayashi, Natsuko I.

    2015-01-01

    Magnesium ions (Mg2+) are the second most abundant cations in living plant cells, and they are involved in various functions, including photosynthesis, enzyme catalysis, and nucleic acid synthesis. Low availability of Mg2+ in an agricultural field leads to a decrease in yield, which follows the appearance of Mg-deficient symptoms such as chlorosis, necrotic spots on the leaves, and droop. During the last decade, a variety of physiological and molecular responses to Mg2+ deficiency that potentially link to leaf senescence have been recognized, allowing us to reconsider the mechanisms of Mg2+ deficiency. This review focuses on the current knowledge about the physiological responses to Mg2+ deficiency including a decline in transpiration, accumulation of sugars and starch in source leaves, change in redox states, increased oxidative stress, metabolite alterations, and a decline in photosynthetic activity. In addition, we refer to the molecular responses that are thought to be related to leaf senescence. With these current data, we give an overview of leaf senescence induced by Mg deficiency. PMID:27135350

  8. Children's and Adults' Judgments of the Certainty of Deductive Inferences, Inductive Inferences, and Guesses

    ERIC Educational Resources Information Center

    Pillow, Bradford H.; Pearson, RaeAnne M.; Hecht, Mary; Bremer, Amanda

    2010-01-01

    Children and adults rated their own certainty following inductive inferences, deductive inferences, and guesses. Beginning in kindergarten, participants rated deductions as more certain than weak inductions or guesses. Deductions were rated as more certain than strong inductions beginning in Grade 3, and fourth-grade children and adults…

  9. The Observation/Inference Chart: Improving Students' Abilities to Make Inferences while Reading Nontraditional Texts

    ERIC Educational Resources Information Center

    Nokes, Jeffery D.

    2008-01-01

    The Observation/Inference (OI) Chart is a strategy that can help students learn to make observations and inferences when reading nontraditional texts such as artifacts, paintings or movies. Nontraditional texts can be highly engaging and provide authentic thinking experiences for students, but they can also be difficult to comprehend. Teachers can…

  10. Using Alien Coins to Test Whether Simple Inference Is Bayesian

    ERIC Educational Resources Information Center

    Cassey, Peter; Hawkins, Guy E.; Donkin, Chris; Brown, Scott D.

    2016-01-01

    Reasoning and inference are well-studied aspects of basic cognition that have been explained as statistically optimal Bayesian inference. Using a simplified experimental design, we conducted quantitative comparisons between Bayesian inference and human inference at the level of individuals. In 3 experiments, with more than 13,000 participants, we…

  11. Dynamical inference of hidden biological populations

    NASA Astrophysics Data System (ADS)

    Luchinsky, D. G.; Smelyanskiy, V. N.; Millonas, M.; McClintock, P. V. E.

    2008-10-01

    Population fluctuations in a predator-prey system are analyzed for the case where the number of prey could be determined, subject to measurement noise, but the number of predators was unknown. The problem of how to infer the unmeasured predator dynamics, as well as the model parameters, is addressed. Two solutions are suggested. In the first of these, measurement noise and the dynamical noise in the equation for predator population are neglected; the problem is reduced to a one-dimensional case, and a Bayesian dynamical inference algorithm is employed to reconstruct the model parameters. In the second solution a full-scale Markov Chain Monte Carlo simulation is used to infer both the unknown predator trajectory, and also the model parameters, using the one-dimensional solution as an initial guess.

  12. Inferences from counterfactual threats and promises.

    PubMed

    Egan, Suzanne M; Byrne, Ruth M J

    2012-01-01

    We examine how people understand and reason from counterfactual threats, for example, "if you had hit your sister, I would have grounded you" and counterfactual promises, for example, "if you had tidied your room, I would have given you ice-cream." The first experiment shows that people consider counterfactual threats, but not counterfactual promises, to have the illocutionary force of an inducement. They also make the immediate inference that the action mentioned in the "if" part of the counterfactual threat and promise did not occur. The second experiment shows that people make more negative inferences (modus tollens and denial of the antecedent) than affirmative inferences (modus ponens and affirmation of the consequent) from counterfactual threats and promises, unlike indicative threats and promises. We discuss the implications of the results for theories of the mental representations and cognitive processes that underlie conditional inducements. PMID:22580411

  13. Identification and Inference for Econometric Models

    NASA Astrophysics Data System (ADS)

    Andrews, Donald W. K.; Stock, James H.

    2005-07-01

    This volume contains the papers presented in honor of the lifelong achievements of Thomas J. Rothenberg on the occasion of his retirement. The authors of the chapters include many of the leading econometricians of our day, and the chapters address topics of current research significance in econometric theory. The chapters cover four themes: identification and efficient estimation in econometrics, asymptotic approximations to the distributions of econometric estimators and tests, inference involving potentially nonstationary time series, such as processes that might have a unit autoregressive root, and nonparametric and semiparametric inference. Several of the chapters provide overviews and treatments of basic conceptual issues, while others advance our understanding of the properties of existing econometric procedures and/or propose new ones. Specific topics include identification in nonlinear models, inference with weak instruments, tests for nonstationary in time series and panel data, generalized empirical likelihood estimation, and the bootstrap.

  14. Parameter inference with estimated covariance matrices

    NASA Astrophysics Data System (ADS)

    Sellentin, Elena; Heavens, Alan F.

    2016-02-01

    When inferring parameters from a Gaussian-distributed data set by computing a likelihood, a covariance matrix is needed that describes the data errors and their correlations. If the covariance matrix is not known a priori, it may be estimated and thereby becomes a random object with some intrinsic uncertainty itself. We show how to infer parameters in the presence of such an estimated covariance matrix, by marginalizing over the true covariance matrix, conditioned on its estimated value. This leads to a likelihood function that is no longer Gaussian, but rather an adapted version of a multivariate t-distribution, which has the same numerical complexity as the multivariate Gaussian. As expected, marginalization over the true covariance matrix improves inference when compared with Hartlap et al.'s method, which uses an unbiased estimate of the inverse covariance matrix but still assumes that the likelihood is Gaussian.

  15. Single board system for fuzzy inference

    NASA Technical Reports Server (NTRS)

    Symon, James R.; Watanabe, Hiroyuki

    1991-01-01

    The very large scale integration (VLSI) implementation of a fuzzy logic inference mechanism allows the use of rule-based control and decision making in demanding real-time applications. Researchers designed a full custom VLSI inference engine. The chip was fabricated using CMOS technology. The chip consists of 688,000 transistors of which 476,000 are used for RAM memory. The fuzzy logic inference engine board system incorporates the custom designed integrated circuit into a standard VMEbus environment. The Fuzzy Logic system uses Transistor-Transistor Logic (TTL) parts to provide the interface between the Fuzzy chip and a standard, double height VMEbus backplane, allowing the chip to perform application process control through the VMEbus host. High level C language functions hide details of the hardware system interface from the applications level programmer. The first version of the board was installed on a robot at Oak Ridge National Laboratory in January of 1990.

  16. Automatic transformations in the inference process

    SciTech Connect

    Veroff, R. L.

    1980-07-01

    A technique for incorporating automatic transformations into processes such as the application of inference rules, subsumption, and demodulation provides a mechanism for improving search strategies for theorem proving problems arising from the field of program verification. The incorporation of automatic transformations into the inference process can alter the search space for a given problem, and is particularly useful for problems having broad rather than deep proofs. The technique can also be used to permit the generation of inferences that might otherwise be blocked and to build some commutativity or associativity into the unification process. Appropriate choice of transformations, and new literal clashing and unification algorithms for applying them, showed significant improvement on several real problems according to several distinct criteria. 22 references, 1 figure.

  17. Binding of inferred germline precursors of broadly neutralizing HIV-1 antibodies to native-like envelope trimers

    PubMed Central

    Sliepen, Kwinten; Medina-Ramírez, Max; Yasmeen, Anila; Moore, John P.; Klasse, Per Johan; Sanders, Rogier W.

    2016-01-01

    HIV-1 envelope glycoproteins (Env) and Env-based immunogens usually do not interact efficiently with the inferred germline precursors of known broadly neutralizing antibodies (bNAbs). This deficiency may be one reason why Env and Env-based immunogens are not efficient at inducing bNAbs. We evaluated the binding of 15 inferred germline precursors of bNAbs directed to different epitope clusters to three soluble native-like SOSIP.664 Env trimers. We found that native-like SOSIP.664 trimers bind to some inferred germline precursors of bNAbs, particularly ones involving the V1/V2 loops at the apex of the trimer. The data imply that native-like SOSIP.664 trimers will be an appropriate platform for structure-guided design improvements intended to create immunogens able to target the germline precursors of bNAbs. PMID:26433050

  18. A formal model of interpersonal inference

    PubMed Central

    Moutoussis, Michael; Trujillo-Barreto, Nelson J.; El-Deredy, Wael; Dolan, Raymond J.; Friston, Karl J.

    2014-01-01

    Introduction: We propose that active Bayesian inference—a general framework for decision-making—can equally be applied to interpersonal exchanges. Social cognition, however, entails special challenges. We address these challenges through a novel formulation of a formal model and demonstrate its psychological significance. Method: We review relevant literature, especially with regards to interpersonal representations, formulate a mathematical model and present a simulation study. The model accommodates normative models from utility theory and places them within the broader setting of Bayesian inference. Crucially, we endow people's prior beliefs, into which utilities are absorbed, with preferences of self and others. The simulation illustrates the model's dynamics and furnishes elementary predictions of the theory. Results: (1) Because beliefs about self and others inform both the desirability and plausibility of outcomes, in this framework interpersonal representations become beliefs that have to be actively inferred. This inference, akin to “mentalizing” in the psychological literature, is based upon the outcomes of interpersonal exchanges. (2) We show how some well-known social-psychological phenomena (e.g., self-serving biases) can be explained in terms of active interpersonal inference. (3) Mentalizing naturally entails Bayesian updating of how people value social outcomes. Crucially this includes inference about one's own qualities and preferences. Conclusion: We inaugurate a Bayes optimal framework for modeling intersubject variability in mentalizing during interpersonal exchanges. Here, interpersonal representations are endowed with explicit functional and affective properties. We suggest the active inference framework lends itself to the study of psychiatric conditions where mentalizing is distorted. PMID:24723872

  19. Pagophagia in iron deficiency anemia.

    PubMed

    Uchida, Tatsumi; Kawati, Yasunori

    2014-04-01

    The relationship between pagophagia (ice pica) and iron deficiency anemia was studied. All 81 patients with iron deficiency anemia defined as hemoglobin <12.0 g/dl and ferritin level <12 ng/ml were interviewed about their habits of eating ice or other non-food substances. Pagophagia was defined as compulsive and repeated ingestion of at least one tray of ice or ice eating which was relieved after iron administration. Pagophagia was present in 13 patients (16.0%). All patients who received oral iron were periodically assessed employing a questionnaire on pagophagia and laboratory data. Iron therapy can cure the pagophagia earlier than hemoglobin recovery and repair of tissue iron deficiency. Although the pathogenesis of pagophagia is unclear, a biochemical approach involving the central nervous system might elucidate the mechanism underlying these abnormal behaviors. PMID:24850454

  20. Glucose-6-Phosphate Dehydrogenase Deficiency.

    PubMed

    Luzzatto, Lucio; Nannelli, Caterina; Notaro, Rosario

    2016-04-01

    G6PD is a housekeeping gene expressed in all cells. Glucose-6-phosphate dehydrogenase (G6PD) is part of the pentose phosphate pathway, and its main physiologic role is to provide NADPH. G6PD deficiency, one of the commonest inherited enzyme abnormalities in humans, arises through one of many possible mutations, most of which reduce the stability of the enzyme and its level as red cells age. G6PD-deficient persons are mostly asymptomatic, but they can develop severe jaundice during the neonatal period and acute hemolytic anemia when they ingest fava beans or when they are exposed to certain infections or drugs. G6PD deficiency is a global health issue. PMID:27040960

  1. Gene-network inference by message passing

    NASA Astrophysics Data System (ADS)

    Braunstein, A.; Pagnani, A.; Weigt, M.; Zecchina, R.

    2008-01-01

    The inference of gene-regulatory processes from gene-expression data belongs to the major challenges of computational systems biology. Here we address the problem from a statistical-physics perspective and develop a message-passing algorithm which is able to infer sparse, directed and combinatorial regulatory mechanisms. Using the replica technique, the algorithmic performance can be characterized analytically for artificially generated data. The algorithm is applied to genome-wide expression data of baker's yeast under various environmental conditions. We find clear cases of combinatorial control, and enrichment in common functional annotations of regulated genes and their regulators.

  2. Inference System Integration Via Logic Morphisms

    NASA Technical Reports Server (NTRS)

    Bjorner, Nikolaj S.; Espinosa, David

    2000-01-01

    This is a final report on the accomplishments during the period of the NASA grant. The work on inference servers accomplished the integration of the SLANG logic (Specware's default specification logic) with a number of inference servers in order to make their complementary strengths available. These inverence servers are (1) SNARK. (2) Gandalf, Setheo, and Spass, (3) the Prototype Verification System (PVS) from SRI. (4) HOL98. We designed and implemented MetaSlang, an ML-like language, which we are using to specify and implement all our logic morphisms.

  3. Iron deficiency in the tropics.

    PubMed

    Fleming, A F

    1982-06-01

    Iron in food is classified as belonging to the haem pool, the nonhaem pool, and extraneous sources. Haem iron is derived from vegetable and animal sources with varying bioavailability. Hookworm infestation of the intestinal tract affects 450 million people in the tropics. Schistosoma mansoni caused blood loss in 7 Egyptian patients of 7.5- 25.9 ml/day which is equivalent to a daily loss of iron of .6-7.3 mg daily urinary loss of iron in 9 Egyptian patients. Trichuris trichiura infestation by whipworm is widespread in children with blood loss of 5 ml/day/worm. The etiology of anemia in children besides iron deficiency includes malaria, bacterial or viral infections, folate deficiency and sickle-cell disease. Severe infections cause profound iron-deficiency anemia in children in central American and Malaysia. Plasmodium falciparum malaria-induced anaemia in tropical Africa lowers the mean haemoglobin concentration in the population by 2 g/dI, causing profound anaemia in some. The increased risk of premature delivery, low birthweight, fetal abnormalities, and fetal death is directly related to the degree of maternal anemia. Perinatal mortality was reduced from 38 to 4% in treated anemic mothers. Mental performance was significantly lower in anemic school children and improved after they received iron. Supplements of iron, soy-protein, calcium, and vitamins given to villagers with widespread malnutrition, iron deficiency, and hookworm infestation in Colombia reduced enteric infections in children. Severe iron-deficiency anemia was treated in adults in northern Nigeria by daily in Ferastral 10 ml, which is equivalent to 500 mg of iron per day. Choloroquine, folic acid, rephenium hydroxynaphthoate, and tetrachlorethylene treat adults with severe iron deficiency from hookworm infestation in rural tropical Africa. Blood transfusion is indicated if the patient is dying of anaemia or is pregnant with a haemoglobin concentration 6 gm/dl. In South East Asia, mg per day

  4. [Phosphate metabolism and iron deficiency].

    PubMed

    Yokoyama, Keitaro

    2016-02-01

    Autosomal dominant hypophosphatemic rickets(ADHR)is caused by gain-of-function mutations in FGF23 that prevent its proteolytic cleavage. Fibroblast growth factor 23(FGF23)is a hormone that inhibits renal phosphate reabsorption and 1,25-dihydroxyvitamin D biosynthesis. Low iron status plays a role in the pathophysiology of ADHR. Iron deficiency is an environmental trigger that stimulates FGF23 expression and hypophosphatemia in ADHR. It was reported that FGF23 elevation in patients with CKD, who are often iron deficient. In patients with nondialysis-dependent CKD, treatment with ferric citrate hydrate resulted in significant reductions in serum phosphate and FGF23. PMID:26813504

  5. Causal Inferences with Group Based Trajectory Models

    ERIC Educational Resources Information Center

    Haviland, Amelia M.; Nagin, Daniel S.

    2005-01-01

    A central theme of research on human development and psychopathology is whether a therapeutic intervention or a turning-point event, such as a family break-up, alters the trajectory of the behavior under study. This paper lays out and applies a method for using observational longitudinal data to make more confident causal inferences about the…

  6. What Children Infer from Social Categories

    ERIC Educational Resources Information Center

    Diesendruck, Gil; Eldror, Ehud

    2011-01-01

    Children hold the belief that social categories have essences. We investigated what kinds of properties children feel licensed to infer about a person based on social category membership. Seventy-two 4-6-year-olds were introduced to novel social categories defined as having one internal--psychological or biological--and one external--behavioral or…

  7. Inference and the Introductory Statistics Course

    ERIC Educational Resources Information Center

    Pfannkuch, Maxine; Regan, Matt; Wild, Chris; Budgett, Stephanie; Forbes, Sharleen; Harraway, John; Parsonage, Ross

    2011-01-01

    This article sets out some of the rationale and arguments for making major changes to the teaching and learning of statistical inference in introductory courses at our universities by changing from a norm-based, mathematical approach to more conceptually accessible computer-based approaches. The core problem of the inferential argument with its…

  8. Making statistical inferences about software reliability

    NASA Technical Reports Server (NTRS)

    Miller, Douglas R.

    1988-01-01

    Failure times of software undergoing random debugging can be modelled as order statistics of independent but nonidentically distributed exponential random variables. Using this model inferences can be made about current reliability and, if debugging continues, future reliability. This model also shows the difficulty inherent in statistical verification of very highly reliable software such as that used by digital avionics in commercial aircraft.

  9. Making statistical inferences about software reliability

    NASA Technical Reports Server (NTRS)

    Miller, Douglas R.

    1986-01-01

    Failure times of software undergoing random debugging can be modeled as order statistics of independent but nonidentically distributed exponential random variables. Using this model inferences can be made about current reliability and, if debugging continues, future reliability. This model also shows the difficulty inherent in statistical verification of very highly reliable software such as that used by digital avionics in commercial aircraft.

  10. Elaborative Inferences on an Expository Text.

    ERIC Educational Resources Information Center

    Durgunoglu, Aydin Y.; Jehng, Jihn-Chang J.

    1991-01-01

    The distinction between remembering text information and applying the acquired knowledge (making inferences) was studied with a dissociation paradigm, using 110 undergraduates who performed verification and recognition tasks. The same variables did not affect performance on the two tasks. Text organization affected recognition but not verification…

  11. Inverse Ising inference with correlated samples

    NASA Astrophysics Data System (ADS)

    Obermayer, Benedikt; Levine, Erel

    2014-12-01

    Correlations between two variables of a high-dimensional system can be indicative of an underlying interaction, but can also result from indirect effects. Inverse Ising inference is a method to distinguish one from the other. Essentially, the parameters of the least constrained statistical model are learned from the observed correlations such that direct interactions can be separated from indirect correlations. Among many other applications, this approach has been helpful for protein structure prediction, because residues which interact in the 3D structure often show correlated substitutions in a multiple sequence alignment. In this context, samples used for inference are not independent but share an evolutionary history on a phylogenetic tree. Here, we discuss the effects of correlations between samples on global inference. Such correlations could arise due to phylogeny but also via other slow dynamical processes. We present a simple analytical model to address the resulting inference biases, and develop an exact method accounting for background correlations in alignment data by combining phylogenetic modeling with an adaptive cluster expansion algorithm. We find that popular reweighting schemes are only marginally effective at removing phylogenetic bias, suggest a rescaling strategy that yields better results, and provide evidence that our conclusions carry over to the frequently used mean-field approach to the inverse Ising problem.

  12. Inference and Children's Comprehension of Pronouns.

    ERIC Educational Resources Information Center

    Wykes, Til

    1981-01-01

    Investigated five-year-olds' abilities to determine the reference of anaphoric pronouns. Children had difficulty when a sentence contained more than one pronoun, especially when assigning the reference of a pronoun requiring an inference. The children's difficulties stemmed from forgetting premise information and from having problems in carrying…

  13. Efficient Bayesian inference for ARFIMA processes

    NASA Astrophysics Data System (ADS)

    Graves, T.; Gramacy, R. B.; Franzke, C. L. E.; Watkins, N. W.

    2015-03-01

    Many geophysical quantities, like atmospheric temperature, water levels in rivers, and wind speeds, have shown evidence of long-range dependence (LRD). LRD means that these quantities experience non-trivial temporal memory, which potentially enhances their predictability, but also hampers the detection of externally forced trends. Thus, it is important to reliably identify whether or not a system exhibits LRD. In this paper we present a modern and systematic approach to the inference of LRD. Rather than Mandelbrot's fractional Gaussian noise, we use the more flexible Autoregressive Fractional Integrated Moving Average (ARFIMA) model which is widely used in time series analysis, and of increasing interest in climate science. Unlike most previous work on the inference of LRD, which is frequentist in nature, we provide a systematic treatment of Bayesian inference. In particular, we provide a new approximate likelihood for efficient parameter inference, and show how nuisance parameters (e.g. short memory effects) can be integrated over in order to focus on long memory parameters, and hypothesis testing more directly. We illustrate our new methodology on the Nile water level data, with favorable comparison to the standard estimators.

  14. Tactile length contraction as Bayesian inference.

    PubMed

    Tong, Jonathan; Ngo, Vy; Goldreich, Daniel

    2016-08-01

    To perceive, the brain must interpret stimulus-evoked neural activity. This is challenging: The stochastic nature of the neural response renders its interpretation inherently uncertain. Perception would be optimized if the brain used Bayesian inference to interpret inputs in light of expectations derived from experience. Bayesian inference would improve perception on average but cause illusions when stimuli violate expectation. Intriguingly, tactile, auditory, and visual perception are all prone to length contraction illusions, characterized by the dramatic underestimation of the distance between punctate stimuli delivered in rapid succession; the origin of these illusions has been mysterious. We previously proposed that length contraction illusions occur because the brain interprets punctate stimulus sequences using Bayesian inference with a low-velocity expectation. A novel prediction of our Bayesian observer model is that length contraction should intensify if stimuli are made more difficult to localize. Here we report a tactile psychophysical study that tested this prediction. Twenty humans compared two distances on the forearm: a fixed reference distance defined by two taps with 1-s temporal separation and an adjustable comparison distance defined by two taps with temporal separation t ≤ 1 s. We observed significant length contraction: As t was decreased, participants perceived the two distances as equal only when the comparison distance was made progressively greater than the reference distance. Furthermore, the use of weaker taps significantly enhanced participants' length contraction. These findings confirm the model's predictions, supporting the view that the spatiotemporal percept is a best estimate resulting from a Bayesian inference process. PMID:27121574

  15. John Updike and Norman Mailer: Sport Inferences.

    ERIC Educational Resources Information Center

    Upshaw, Kathryn Jane

    The phenomenon of writer use of sport inferences in the literary genre of the novel is examined in the works of Updike and Mailer. Novels of both authors were reviewed in order to study the pattern of usage in each novel. From these patterns, concepts which illustrated the sport philosophies of each author were used for general comparisons of the…

  16. Campbell's and Rubin's Perspectives on Causal Inference

    ERIC Educational Resources Information Center

    West, Stephen G.; Thoemmes, Felix

    2010-01-01

    Donald Campbell's approach to causal inference (D. T. Campbell, 1957; W. R. Shadish, T. D. Cook, & D. T. Campbell, 2002) is widely used in psychology and education, whereas Donald Rubin's causal model (P. W. Holland, 1986; D. B. Rubin, 1974, 2005) is widely used in economics, statistics, medicine, and public health. Campbell's approach focuses on…

  17. Investigating Mathematics Teachers' Thoughts of Statistical Inference

    ERIC Educational Resources Information Center

    Yang, Kai-Lin

    2012-01-01

    Research on statistical cognition and application suggests that statistical inference concepts are commonly misunderstood by students and even misinterpreted by researchers. Although some research has been done on students' misunderstanding or misconceptions of confidence intervals (CIs), few studies explore either students' or mathematics…

  18. Decision generation tools and Bayesian inference

    NASA Astrophysics Data System (ADS)

    Jannson, Tomasz; Wang, Wenjian; Forrester, Thomas; Kostrzewski, Andrew; Veeris, Christian; Nielsen, Thomas

    2014-05-01

    Digital Decision Generation (DDG) tools are important software sub-systems of Command and Control (C2) systems and technologies. In this paper, we present a special type of DDGs based on Bayesian Inference, related to adverse (hostile) networks, including such important applications as terrorism-related networks and organized crime ones.

  19. Linguistic Markers of Inference Generation While Reading

    ERIC Educational Resources Information Center

    Clinton, Virginia; Carlson, Sarah E.; Seipel, Ben

    2016-01-01

    Words can be informative linguistic markers of psychological constructs. The purpose of this study is to examine associations between word use and the process of making meaningful connections to a text while reading (i.e., inference generation). To achieve this purpose, think-aloud data from third-fifth grade students (N = 218) reading narrative…

  20. Evolutionary inference via the Poisson Indel Process.

    PubMed

    Bouchard-Côté, Alexandre; Jordan, Michael I

    2013-01-22

    We address the problem of the joint statistical inference of phylogenetic trees and multiple sequence alignments from unaligned molecular sequences. This problem is generally formulated in terms of string-valued evolutionary processes along the branches of a phylogenetic tree. The classic evolutionary process, the TKF91 model [Thorne JL, Kishino H, Felsenstein J (1991) J Mol Evol 33(2):114-124] is a continuous-time Markov chain model composed of insertion, deletion, and substitution events. Unfortunately, this model gives rise to an intractable computational problem: The computation of the marginal likelihood under the TKF91 model is exponential in the number of taxa. In this work, we present a stochastic process, the Poisson Indel Process (PIP), in which the complexity of this computation is reduced to linear. The Poisson Indel Process is closely related to the TKF91 model, differing only in its treatment of insertions, but it has a global characterization as a Poisson process on the phylogeny. Standard results for Poisson processes allow key computations to be decoupled, which yields the favorable computational profile of inference under the PIP model. We present illustrative experiments in which Bayesian inference under the PIP model is compared with separate inference of phylogenies and alignments. PMID:23275296

  1. Rates inferred from the space debris catalog

    SciTech Connect

    Canavan, G.H.

    1996-08-01

    Collision and fragmentation rates are inferred from the AFSPC space debris catalog and compare with estimates from other treatments. The collision rate is evaluated without approximation. The fragmentation rate requires additional empirical assessments. The number of fragments per collision is low compared to analytic and numerical treatments, is peaked low, and falls rapidly with altitude.

  2. Causal Inferences in the Campbellian Validity System

    ERIC Educational Resources Information Center

    Lund, Thorleif

    2010-01-01

    The purpose of the present paper is to critically examine causal inferences and internal validity as defined by Campbell and co-workers. Several arguments are given against their counterfactual effect definition, and this effect definition should be considered inadequate for causal research in general. Moreover, their defined independence between…

  3. An evaluation of explanations of probabilistic inference.

    PubMed Central

    Suermondt, H. J.; Cooper, G. F.

    1992-01-01

    Providing explanations of the conclusions of decision-support systems can be viewed as presenting inference results in a manner that enhances the user's insight into how these results were obtained. The ability to explain inferences has been demonstrated to be an important factor in making medical decision-support systems acceptable for clinical use. Although many researchers in artificial intelligence have explored the automatic generation of explanations for decision-support systems based on symbolic reasoning, research in automated explanation of probabilistic results has been limited. We present the results of an an evaluation study of INSITE, a program that explains the reasoning of decision-support systems based on Bayesian belief networks. In the domain of anesthesia, we compared subjects who had access to a belief network with explanations of the inference results, to control subjects who used the same belief network without explanations. We show that, compared to control subjects, the explanation subjects demonstrated greater diagnostic accuracy, were more confident about their conclusions, were more critical of the belief network, and found the presentation of the inference results more clear. PMID:1482939

  4. Connecting Scientific Reasoning and Causal Inference

    ERIC Educational Resources Information Center

    Kuhn, Deanna; Dean, David, Jr.

    2004-01-01

    Literature on multivariable causal inference (MCI) and literature on scientific reasoning (SR) have proceeded almost entirely independently, although they in large part address the same phenomena. An effort is made to bring these paradigms into close enough alignment with one another to compare implications of the two lines of work and examine how…

  5. Statistical Inference in Retrieval Effectiveness Evaluation.

    ERIC Educational Resources Information Center

    Savoy, Jacques

    1997-01-01

    Discussion of evaluation methodology in information retrieval focuses on the average precision over a set of fixed recall values in an effort to evaluate the retrieval effectiveness of a search algorithm. Highlights include a review of traditional evaluation methodology with examples; and a statistical inference methodology called bootstrap.…

  6. Pediatric Pain, Predictive Inference, and Sensitivity Analysis.

    ERIC Educational Resources Information Center

    Weiss, Robert

    1994-01-01

    Coping style and effects of counseling intervention on pain tolerance was studied for 61 elementary school students through immersion of hands in cold water. Bayesian predictive inference tools are able to distinguish between subject characteristics and manipulable treatments. Sensitivity analysis strengthens the certainty of conclusions about…

  7. Double jeopardy in inferring cognitive processes

    PubMed Central

    Fific, Mario

    2014-01-01

    Inferences we make about underlying cognitive processes can be jeopardized in two ways due to problematic forms of aggregation. First, averaging across individuals is typically considered a very useful tool for removing random variability. The threat is that averaging across subjects leads to averaging across different cognitive strategies, thus harming our inferences. The second threat comes from the construction of inadequate research designs possessing a low diagnostic accuracy of cognitive processes. For that reason we introduced the systems factorial technology (SFT), which has primarily been designed to make inferences about underlying processing order (serial, parallel, coactive), stopping rule (terminating, exhaustive), and process dependency. SFT proposes that the minimal research design complexity to learn about n number of cognitive processes should be equal to 2n. In addition, SFT proposes that (a) each cognitive process should be controlled by a separate experimental factor, and (b) The saliency levels of all factors should be combined in a full factorial design. In the current study, the author cross combined the levels of jeopardies in a 2 × 2 analysis, leading to four different analysis conditions. The results indicate a decline in the diagnostic accuracy of inferences made about cognitive processes due to the presence of each jeopardy in isolation and when combined. The results warrant the development of more individual subject analyses and the utilization of full-factorial (SFT) experimental designs. PMID:25374545

  8. Management of Iron Deficiency Anemia

    PubMed Central

    Jimenez, Kristine; Kulnigg-Dabsch, Stefanie

    2015-01-01

    Anemia affects one-fourth of the world’s population, and iron deficiency is the predominant cause. Anemia is associated with chronic fatigue, impaired cognitive function, and diminished well-being. Patients with iron deficiency anemia of unknown etiology are frequently referred to a gastroenterologist because in the majority of cases the condition has a gastrointestinal origin. Proper management improves quality of life, alleviates the symptoms of iron deficiency, and reduces the need for blood transfusions. Treatment options include oral and intravenous iron therapy; however, the efficacy of oral iron is limited in certain gastrointestinal conditions, such as inflammatory bowel disease, celiac disease, and autoimmune gastritis. This article provides a critical summary of the diagnosis and treatment of iron deficiency anemia. In addition, it includes a management algorithm that can help the clinician determine which patients are in need of further gastrointestinal evaluation. This facilitates the identification and treatment of the underlying condition and avoids the unnecessary use of invasive methods and their associated risks. PMID:27099596

  9. Dopamine beta-hydroxylase deficiency

    PubMed Central

    Senard, Jean-Michel; Rouet, Philippe

    2006-01-01

    Dopamine beta-hydroxylase (DβH) deficiency is a very rare form of primary autonomic failure characterized by a complete absence of noradrenaline and adrenaline in plasma together with increased dopamine plasma levels. The prevalence of DβH deficiency is unknown. Only a limited number of cases with this disease have been reported. DβH deficiency is mainly characterized by cardiovascular disorders and severe orthostatic hypotension. First symptoms often start during a complicated perinatal period with hypotension, muscle hypotonia, hypothermia and hypoglycemia. Children with DβH deficiency exhibit reduced ability to exercise because of blood pressure inadaptation with exertion and syncope. Symptoms usually worsen progressively during late adolescence and early adulthood with severe orthostatic hypotension, eyelid ptosis, nasal stuffiness and sexual disorders. Limitation in standing tolerance, limited ability to exercise and traumatic morbidity related to falls and syncope may represent later evolution. The syndrome is caused by heterogeneous molecular alterations of the DBH gene and is inherited in an autosomal recessive manner. Restoration of plasma noradrenaline to the normal range can be achieved by therapy with the synthetic precursor of noradrenaline, L-threo-dihydroxyphenylserine (DOPS). Oral administration of 100 to 500 mg DOPS, twice or three times daily, increases blood pressure and reverses the orthostatic intolerance. PMID:16722595

  10. Iodine deficiency disorders in Bangladesh.

    PubMed

    Yusuf, H K; Quazi, S; Kahn, M R; Mohiduzzaman, M; Nahar, B; Rahman, M M; Islam, M N; Khan, M A; Shahidullah, M; Hoque, T; Baquer, M; Pandav, C S

    1996-01-01

    An extensive iodine deficiency disorders survey was conducted in Bangladesh in 1993 to assess the latest iodine nutriture status of the country. The clinical variables of the survey were goitre and cretinism, and the biochemical variable was urinary iodine. The "EPI-30 cluster" sampling methodology was followed for selecting the survey sites. In each survey site, the study population consisted of boys and girls, aged 5-11 years, and men and women, aged 15-44 years, in about equal populations. The total number of survey sites was 78 and the total number of respondents was 30,072. The total number of urine samples was 4512 (15% sub-sample). The current total goitre rate (grade 1 + grade 2) in Bangladesh is 47.1% (hilly, 44.4%; flood-prone, 50.7%; and plains, 45.6%). The prevalence of cretinism in the country is 0.5% (hilly, 0.8%; flood-prone, 0.5%; and plains, 0.3%). Nearly 69% of Bangladeshi population have biochemical iodine deficiency (urinary iodine excretion [UIE] < 10 mg/dl) (hilly, 84.4; flood-prone, 67.1%; and plains 60.4%). Women and children are more affected that men, in terms of both goitre prevalence and UIE. The widespread severe iodine deficiency in all ecological zones indicates that the country as a whole is an iodine-deficient region. Important recommendations of global interest are made from the experience of the survey. PMID:10829973

  11. Growth hormone deficiency: an update.

    PubMed

    Audí, L; Fernández-Cancio, M; Camats, N; Carrascosa, A

    2013-03-01

    Growth hormone (GH) deficiency (GHD) in humans manifests differently according to the individual developmental stage (early after birth, during childhood, at puberty or in adulthood), the cause or mechanism (genetic, acquired or idiopathic), deficiency intensity and whether it is the only pituitary-affected hormone or is combined with that of other pituitary hormones or forms part of a complex syndrome. Growing knowledge of the genetic basis of GH deficiency continues to provide us with useful information to further characterise mutation types and mechanisms for previously described and new candidate genes. Despite these advances, a high proportion of GH deficiencies with no recognisable acquired basis continue to be labelled as idiopathic, although less frequently when they are congenital and/or familial. The clinical and biochemical diagnoses continue to be a conundrum despite efforts to harmonise biochemical assays for GH and IGF-1 analysis, probably because the diagnosis based on the so-called GH secretion stimulation tests will prove to be of limited usefulness for predicting therapy indications. PMID:23435439

  12. VISUAL DEFICIENCIES AND READING DISABILITY.

    ERIC Educational Resources Information Center

    ROSEN, CARL L.

    THE ROLE OF VISUAL SENSORY DEFICIENCIES IN THE CAUSATION READING DISABILITY IS DISCUSSED. PREVIOUS AND CURRENT RESEARCH STUDIES DEALING WITH SPECIFIC VISUAL PROBLEMS WHICH HAVE BEEN FOUND TO BE NEGATIVELY RELATED TO SUCCESSFUL READING ACHIEVEMENT ARE LISTED--(1) FARSIGHTEDNESS, (2) ASTIGMATISM, (3) BINOCULAR INCOORDINATIONS, AND (4) FUSIONAL…

  13. Psychological Problems in Mental Deficiency.

    ERIC Educational Resources Information Center

    Sarason, Seymour B.; Doris, John

    A statement of goals and the rationale for organization precede a historical discussion of mental deficiency and society. The problem of labels like IQ and brain injured and the consequences of the diagnostic process are illustrated by case histories; case studies are also used to examine the criteria used to decide who is retarded and to discuss…

  14. Reliability of inferred age, and coincidence between inferred age and chronological age.

    PubMed

    Kataoka, J; Ohara, S; Shibata, S; Maie, K

    1996-06-01

    Outdoor research is restricted by many factors. The age inference was one of the biggest problems for the outdoor researchers. We have investigated the reliability of inferred age for the Japanese people, and took out the estimation formula for the age, even if it was based on the inferred age. The age classification was the most popular method for this purpose, and there were many classifications. We took the classification of young, middle aged, and elderly groups, in which classification of the SDs were rather small, that is, 4, 5, and 7 years for the young, middle aged, and elderly age groups, respectively. PMID:9551138

  15. Micronutrient deficiency in urban Indonesia.

    PubMed

    Gross, R; Schultink, W

    1997-06-01

    The economic situation of Indonesia is characterized by a large increase in the gross national product which has been on average 7% annually during the last ten years. This was accompanied by rapid urbanization. With the economic improvement, "First World" and "Third World" health and nutrition problems are coexisting in Indonesia. In 1992, the most common of death cause was cardiovascular disease whereas tuberculosis was the second ranking. About 40% of the preschool children are stunted. The main stable food and energy source is rice, although the urban population has a more diverse food pattern than the rural population. In Jakarta, many children receive too late colostrum feeding and mothers are not aware about the importance of correct breastfeeding practices after delivery. Three studies had shown that about one fifth of preschool children and one fourth of elderly take micronutrient supplements. Nevertheless, micronutrient deficiencies are prevalent in Jakarta. About one third of women suffer from moderate vitamin A deficiency (plasma retinol < 0.70 mmol/L) and 50% of pregnant women are anemic. More information is necessary on other micronutrient deficiencies. For example, a small study revealed that nearly two thirds of non-institutionalized elderly living in Jakarta experience thiamine deficiency. Appropriate interventions to reduce micronutrient deficiencies should sensitize the urban population to the fact that the government should restrict itself to use its resources to assist only the poorest individuals and groups, whereas it must be expected from the middle class to spend more time and money to solve their own problems. PMID:9659420

  16. Iron refractory iron deficiency anemia

    PubMed Central

    De Falco, Luigia; Sanchez, Mayka; Silvestri, Laura; Kannengiesser, Caroline; Muckenthaler, Martina U.; Iolascon, Achille; Gouya, Laurent; Camaschella, Clara; Beaumont, Carole

    2013-01-01

    Iron refractory iron deficiency anemia is a hereditary recessive anemia due to a defect in the TMPRSS6 gene encoding Matriptase-2. This protein is a transmembrane serine protease that plays an essential role in down-regulating hepcidin, the key regulator of iron homeostasis. Hallmarks of this disease are microcytic hypochromic anemia, low transferrin saturation and normal/high serum hepcidin values. The anemia appears in the post-natal period, although in some cases it is only diagnosed in adulthood. The disease is refractory to oral iron treatment but shows a slow response to intravenous iron injections and partial correction of the anemia. To date, 40 different Matriptase-2 mutations have been reported, affecting all the functional domains of the large ectodomain of the protein. In vitro experiments on transfected cells suggest that Matriptase-2 cleaves Hemojuvelin, a major regulator of hepcidin expression and that this function is altered in this genetic form of anemia. In contrast to the low/undetectable hepcidin levels observed in acquired iron deficiency, in patients with Matriptase-2 deficiency, serum hepcidin is inappropriately high for the low iron status and accounts for the absent/delayed response to oral iron treatment. A challenge for the clinicians and pediatricians is the recognition of the disorder among iron deficiency and other microcytic anemias commonly found in pediatric patients. The current treatment of iron refractory iron deficiency anemia is based on parenteral iron administration; in the future, manipulation of the hepcidin pathway with the aim of suppressing it might become an alternative therapeutic approach. PMID:23729726

  17. Genetics Home Reference: complement factor I deficiency

    MedlinePlus

    ... Page Baracho GV, Nudelman V, Isaac L. Molecular characterization of homozygous hereditary factor I deficiency. Clin Exp ... G, Sánchez-Corral P, López-Trascasa M. Molecular characterization of Complement Factor I deficiency in two Spanish ...

  18. Genetics Home Reference: GM3 synthase deficiency

    MedlinePlus

    ... GM3 synthase deficiency is characterized by recurrent seizures (epilepsy) and problems with brain development. Within the first ... diagnosis or management of GM3 synthase deficiency: American Epilepsy Society: Find a Doctor Clinic for Special Children ( ...

  19. Genetics Home Reference: familial glucocorticoid deficiency

    MedlinePlus

    ... familial glucocorticoid deficiency type 1 lead to defective trafficking of the receptor to the cell surface. J ... short stature, and natural killer cell deficiency in humans. J Clin Invest. 2012 Mar;122(3):814- ...

  20. Genetics Home Reference: 21-hydroxylase deficiency

    MedlinePlus

    ... deficiency is an inherited disorder that affects the adrenal glands . The adrenal glands are located on top of the kidneys and ... body. In people with 21-hydroxylase deficiency , the adrenal glands produce excess androgens, which are male sex hormones. ...

  1. Monocular Elevation Deficiency - Double Elevator Palsy

    MedlinePlus

    ... Eye Terms Conditions Frequently Asked Questions Español Condiciones Chinese Conditions Monocular Elevation Deficiency/ Double Elevator Palsy En Español Read in Chinese What is monocular elevation deficiency (Double Elevator Palsy)? ...

  2. How Is Alpha-1 Antitrypsin Deficiency Treated?

    MedlinePlus

    ... from the NHLBI on Twitter. How Is Alpha-1 Antitrypsin Deficiency Treated? Alpha-1 antitrypsin (AAT) deficiency has no cure, but its ... of these treatments are the same as the ones used for a lung disease called COPD (chronic ...

  3. Multiple Carboxylase Deficiency (Late Onset) Due to Deficiency of Biotinidase

    PubMed Central

    Mukhopadhyay, Debadatta; Das, Manoj Kumar; Dhar, Sandipan; Mukhopadhyay, Maya

    2014-01-01

    Biotinidase is a ubiquitous mammalian cell enzyme occurring in liver, serum and kidney. It cleaves biotin from biocytin, which is a cofactor for biotin dependent enzymes, namely the human carboxylases. Biotinidase deficiency is associated with a wide spectrum of neurological, dermatological, immunological and ophthalmological abnormalities. This is a case of a 3-year-old boy presenting with delayed developmental milestones, tachypnea, progressively increasing ataxia, alopecia and dermatitis, all which dramatically responded to high doses of biotin. PMID:25284861

  4. Deficiency or dementia? Exploring B12 deficiency after urostomy.

    PubMed

    Boucher, Michelle; Bryan, Sandra; Dukes, Suzie

    Vitamin B12 deficiency can be misdiagnosed as a variety of other illnesses, and if left untreated can lead to irreversible damage to the brain and nervous system. This article discusses the case of a 70-year-old female with a urostomy, well known to the stoma care department, who shortly after a routine parastomal hernia repair developed severe confusion, immobility and was unable to communicate. Subsequent investigations ruled out a cerebrovascular accident (CVA) and a diagnosis of rapidly progressing vascular dementia was made. An incidental finding of a low vitamin B12 level was identified and treatment commenced. She was transferred to a community hospital and her family were told to 'prepare for the worst'. It was, in fact, the vitamin B12 deficiency that was causing her symptoms of vascular dementia, and once treatment was established she underwent a 'miraculous' improvement, returning to normal life. This article discusses vitamin B12 deficiency and why patients with a urostomy are at risk of developing it; highlights the key role of the stoma care nurse and his or her knowledge of the patient; explores the importance of testing vitamin B12 levels in this group of patients; and discusses key learning and recommendations for practice. PMID:26067796

  5. Iron-induced nickel deficiency in pecan

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Economic loss due to nickel (Ni) deficiency can occur in horticultural and agronomic crops. This study assesses impact of excessive iron (Fe) on expression of Ni deficiency in pecan [Carya illinoinensis (Wangenh.) K. Koch]. Field and greenhouse experiments found Ni deficiency to be inducible by ei...

  6. Iron Deficiency in Autism and Asperger Syndrome.

    ERIC Educational Resources Information Center

    Latif, A.; Heinz, P.; Cook, R.

    2002-01-01

    Retrospective analysis of the full blood count and, when available, serum ferritin measurements of 96 children (52 with autism and 44 with Asperger syndrome) found six autistic children had iron deficiency and 12 of the 23 autistic children with serum ferritin measures were iron deficient. Far fewer Asperger children were iron deficient. Results…

  7. An Intuitive Dashboard for Bayesian Network Inference

    NASA Astrophysics Data System (ADS)

    Reddy, Vikas; Charisse Farr, Anna; Wu, Paul; Mengersen, Kerrie; Yarlagadda, Prasad K. D. V.

    2014-03-01

    Current Bayesian network software packages provide good graphical interface for users who design and develop Bayesian networks for various applications. However, the intended end-users of these networks may not necessarily find such an interface appealing and at times it could be overwhelming, particularly when the number of nodes in the network is large. To circumvent this problem, this paper presents an intuitive dashboard, which provides an additional layer of abstraction, enabling the end-users to easily perform inferences over the Bayesian networks. Unlike most software packages, which display the nodes and arcs of the network, the developed tool organises the nodes based on the cause-and-effect relationship, making the user-interaction more intuitive and friendly. In addition to performing various types of inferences, the users can conveniently use the tool to verify the behaviour of the developed Bayesian network. The tool has been developed using QT and SMILE libraries in C++.

  8. Inference in high-dimensional parameter space.

    PubMed

    O'Hare, Anthony

    2015-11-01

    Model parameter inference has become increasingly popular in recent years in the field of computational epidemiology, especially for models with a large number of parameters. Techniques such as Approximate Bayesian Computation (ABC) or maximum/partial likelihoods are commonly used to infer parameters in phenomenological models that best describe some set of data. These techniques rely on efficient exploration of the underlying parameter space, which is difficult in high dimensions, especially if there are correlations between the parameters in the model that may not be known a priori. The aim of this article is to demonstrate the use of the recently invented Adaptive Metropolis algorithm for exploring parameter space in a practical way through the use of a simple epidemiological model. PMID:26176624

  9. Pointwise probability reinforcements for robust statistical inference.

    PubMed

    Frénay, Benoît; Verleysen, Michel

    2014-02-01

    Statistical inference using machine learning techniques may be difficult with small datasets because of abnormally frequent data (AFDs). AFDs are observations that are much more frequent in the training sample that they should be, with respect to their theoretical probability, and include e.g. outliers. Estimates of parameters tend to be biased towards models which support such data. This paper proposes to introduce pointwise probability reinforcements (PPRs): the probability of each observation is reinforced by a PPR and a regularisation allows controlling the amount of reinforcement which compensates for AFDs. The proposed solution is very generic, since it can be used to robustify any statistical inference method which can be formulated as a likelihood maximisation. Experiments show that PPRs can be easily used to tackle regression, classification and projection: models are freed from the influence of outliers. Moreover, outliers can be filtered manually since an abnormality degree is obtained for each observation. PMID:24300550

  10. Constructing inferences during narrative text comprehension.

    PubMed

    Graesser, A C; Singer, M; Trabasso, T

    1994-07-01

    The authors describe a constructionist theory that accounts for the knowledge-based inferences that are constructed when readers comprehend narrative text. Readers potentially generate a rich variety of inferences when they construct a referential situation model of what the text is about. The proposed constructionist theory specifies that some, but not all, of this information is constructed under most conditions of comprehension. The distinctive assumptions of the constructionist theory embrace a principle of search (or effort) after meaning. According to this principle, readers attempt to construct a meaning representation that addresses the reader's goals, that is coherent at both local and global levels, and that explains why actions, events, and states are mentioned in the text. This study reviews empirical evidence that addresses this theory and contrasts it with alternative theoretical frameworks. PMID:7938337

  11. Dopamine, reward learning, and active inference

    PubMed Central

    FitzGerald, Thomas H. B.; Dolan, Raymond J.; Friston, Karl

    2015-01-01

    Temporal difference learning models propose phasic dopamine signaling encodes reward prediction errors that drive learning. This is supported by studies where optogenetic stimulation of dopamine neurons can stand in lieu of actual reward. Nevertheless, a large body of data also shows that dopamine is not necessary for learning, and that dopamine depletion primarily affects task performance. We offer a resolution to this paradox based on an hypothesis that dopamine encodes the precision of beliefs about alternative actions, and thus controls the outcome-sensitivity of behavior. We extend an active inference scheme for solving Markov decision processes to include learning, and show that simulated dopamine dynamics strongly resemble those actually observed during instrumental conditioning. Furthermore, simulated dopamine depletion impairs performance but spares learning, while simulated excitation of dopamine neurons drives reward learning, through aberrant inference about outcome states. Our formal approach provides a novel and parsimonious reconciliation of apparently divergent experimental findings. PMID:26581305

  12. The NIFTY way of Bayesian signal inference

    SciTech Connect

    Selig, Marco

    2014-12-05

    We introduce NIFTY, 'Numerical Information Field Theory', a software package for the development of Bayesian signal inference algorithms that operate independently from any underlying spatial grid and its resolution. A large number of Bayesian and Maximum Entropy methods for 1D signal reconstruction, 2D imaging, as well as 3D tomography, appear formally similar, but one often finds individualized implementations that are neither flexible nor easily transferable. Signal inference in the framework of NIFTY can be done in an abstract way, such that algorithms, prototyped in 1D, can be applied to real world problems in higher-dimensional settings. NIFTY as a versatile library is applicable and already has been applied in 1D, 2D, 3D and spherical settings. A recent application is the D{sup 3}PO algorithm targeting the non-trivial task of denoising, deconvolving, and decomposing photon observations in high energy astronomy.

  13. Inferring network topology via the propagation process

    NASA Astrophysics Data System (ADS)

    Zeng, An

    2013-11-01

    Inferring the network topology from the dynamics is a fundamental problem, with wide applications in geology, biology, and even counter-terrorism. Based on the propagation process, we present a simple method to uncover the network topology. A numerical simulation on artificial networks shows that our method enjoys a high accuracy in inferring the network topology. We find that the infection rate in the propagation process significantly influences the accuracy, and that each network corresponds to an optimal infection rate. Moreover, the method generally works better in large networks. These finding are confirmed in both real social and nonsocial networks. Finally, the method is extended to directed networks, and a similarity measure specific for directed networks is designed.

  14. Spectral likelihood expansions for Bayesian inference

    NASA Astrophysics Data System (ADS)

    Nagel, Joseph B.; Sudret, Bruno

    2016-03-01

    A spectral approach to Bayesian inference is presented. It pursues the emulation of the posterior probability density. The starting point is a series expansion of the likelihood function in terms of orthogonal polynomials. From this spectral likelihood expansion all statistical quantities of interest can be calculated semi-analytically. The posterior is formally represented as the product of a reference density and a linear combination of polynomial basis functions. Both the model evidence and the posterior moments are related to the expansion coefficients. This formulation avoids Markov chain Monte Carlo simulation and allows one to make use of linear least squares instead. The pros and cons of spectral Bayesian inference are discussed and demonstrated on the basis of simple applications from classical statistics and inverse modeling.

  15. The empirical accuracy of uncertain inference models

    NASA Technical Reports Server (NTRS)

    Vaughan, David S.; Yadrick, Robert M.; Perrin, Bruce M.; Wise, Ben P.

    1987-01-01

    Uncertainty is a pervasive feature of the domains in which expert systems are designed to function. Research design to test uncertain inference methods for accuracy and robustness, in accordance with standard engineering practice is reviewed. Several studies were conducted to assess how well various methods perform on problems constructed so that correct answers are known, and to find out what underlying features of a problem cause strong or weak performance. For each method studied, situations were identified in which performance deteriorates dramatically. Over a broad range of problems, some well known methods do only about as well as a simple linear regression model, and often much worse than a simple independence probability model. The results indicate that some commercially available expert system shells should be used with caution, because the uncertain inference models that they implement can yield rather inaccurate results.

  16. The NIFTy way of Bayesian signal inference

    NASA Astrophysics Data System (ADS)

    Selig, Marco

    2014-12-01

    We introduce NIFTy, "Numerical Information Field Theory", a software package for the development of Bayesian signal inference algorithms that operate independently from any underlying spatial grid and its resolution. A large number of Bayesian and Maximum Entropy methods for 1D signal reconstruction, 2D imaging, as well as 3D tomography, appear formally similar, but one often finds individualized implementations that are neither flexible nor easily transferable. Signal inference in the framework of NIFTy can be done in an abstract way, such that algorithms, prototyped in 1D, can be applied to real world problems in higher-dimensional settings. NIFTy as a versatile library is applicable and already has been applied in 1D, 2D, 3D and spherical settings. A recent application is the D3PO algorithm targeting the non-trivial task of denoising, deconvolving, and decomposing photon observations in high energy astronomy.

  17. Iodine deficiency disorders in Europe.

    PubMed Central

    Delange, F.; Bürgi, H.

    1989-01-01

    Recent data on iodine excretion in the urine of adults, adolescents and newborns and on the iodine content of breast milk indicate a high prevalence of iodine deficiency (moderate in many cases and severe in a few) in many European countries. These cases may manifest as subclinical hypothyroidism in neonates and as goitre in adolescents and adults. Lack of iodine causes not only goitre, but also mental deficiency, hearing loss and other neurological impairments, and short stature due to thyroid insufficiency during fetal development and childhood. Although iodinated salt is available theoretically in most countries where it is needed, its quality and share of the market are often unsatisfactory. In many countries where only household salt is iodinated the iodine content has been set too low owing to an overestimation of household salt consumption. Governments are therefore urged to pass legislation and provide means for efficient iodination of salt wherever this is necessary. PMID:2670299

  18. Iodine: deficiency and therapeutic considerations.

    PubMed

    Patrick, Lyn

    2008-06-01

    Iodine deficiency is generally recognized as the most commonly preventable cause of mental retardation and the most common cause of endocrinopathy (goiter and primary hypothyroidism). Iodine deficiency becomes particularly critical in pregnancy due to the consequences for neurological damage during fetal development as well as during lactation. The safety of therapeutic doses of iodine above the established safe upper limit of 1 mg is evident in the lack of toxicity in the Japanese population that consumes 25 times the median intake of iodine consumption in the United States. Japan's population suffers no demonstrable increased incidence of autoimmune thyroiditis or hypothyroidism. Studies using 3.0- to 6.0-mg doses to effectively treat fibrocystic breast disease may reveal an important role for iodine in maintaining normal breast tissue architecture and function. Iodine may also have important antioxidant functions in breast tissue and other tissues that concentrate iodine via the sodium iodide symporter. PMID:18590348

  19. Iron deficiency anemia in pregnancy.

    PubMed

    Di Renzo, Gian Carlo; Spano, Filippo; Giardina, Irene; Brillo, Eleonora; Clerici, Graziano; Roura, Luis Cabero

    2015-11-01

    Anemia is the most frequent derailment of physiology in the world throughout the life of a woman. It is a serious condition in countries that are industrialized and in countries with poor resources. The main purpose of this manuscript is to give the right concern of anemia in pregnancy. The most common causes of anemia are poor nutrition, iron deficiencies, micronutrients deficiencies including folic acid, vitamin A and vitamin B12, diseases like malaria, hookworm infestation and schistosomiasis, HIV infection and genetically inherited hemoglobinopathies such as thalassemia. Depending on the severity and duration of anemia and the stage of gestation, there could be different adverse effects including low birth weight and preterm delivery. Treatment of mild anemia prevents more severe forms of anemia, strictly associated with increased risk of fetal-maternal mortality and morbidity. PMID:26472066

  20. Impacts of Terraces on Phylogenetic Inference.

    PubMed

    Sanderson, Michael J; McMahon, Michelle M; Stamatakis, Alexandros; Zwickl, Derrick J; Steel, Mike

    2015-09-01

    Terraces are sets of trees with precisely the same likelihood or parsimony score, which can be induced by missing sequences in partitioned multi-locus phylogenetic data matrices. The potentially large set of trees on a terrace can be characterized by enumeration algorithms or consensus methods that exploit the pattern of partial taxon coverage in the data, independent of the sequence data themselves. Terraces can add ambiguity and complexity to phylogenetic inference, particularly in settings where inference is already challenging: data sets with many taxa and relatively few loci. In this article we present five new findings about terraces and their impacts on phylogenetic inference. First, we clarify assumptions about partitioning scheme model parameters that are necessary for the existence of terraces. Second, we explore the dependence of terrace size on partitioning scheme and indicate how to find the partitioning scheme associated with the largest terrace containing a given tree. Third, we highlight the impact of terrace size on bootstrap estimates of confidence limits in clades, and characterize the surprising result that the bootstrap proportion for a clade, as it is usually calculated, can be entirely determined by the frequency of bipartitions on a terrace, with some bipartitions receiving high support even when incorrect. Fourth, we dissect some effects of prior distributions of edge lengths on the computed posterior probabilities of clades on terraces, to understand an example in which long edges "attract" each other in Bayesian inference. Fifth, we describe how assuming relationships between edge-lengths of different loci, as an attempt to avoid terraces, can also be problematic when taxon coverage is partial, specifically when heterotachy is present. Finally, we discuss strategies for remediation of some of these problems. One promising approach finds a minimal set of taxa which, when deleted from the data matrix, reduces the size of a terrace to a

  1. Nonparametric causal inference for bivariate time series

    NASA Astrophysics Data System (ADS)

    McCracken, James M.; Weigel, Robert S.

    2016-02-01

    We introduce new quantities for exploratory causal inference between bivariate time series. The quantities, called penchants and leanings, are computationally straightforward to apply, follow directly from assumptions of probabilistic causality, do not depend on any assumed models for the time series generating process, and do not rely on any embedding procedures; these features may provide a clearer interpretation of the results than those from existing time series causality tools. The penchant and leaning are computed based on a structured method for computing probabilities.

  2. Scalable Probabilistic Inference for Global Seismic Monitoring

    NASA Astrophysics Data System (ADS)

    Arora, N. S.; Dear, T.; Russell, S.

    2011-12-01

    We describe a probabilistic generative model for seismic events, their transmission through the earth, and their detection (or mis-detection) at seismic stations. We also describe an inference algorithm that constructs the most probable event bulletin explaining the observed set of detections. The model and inference are called NET-VISA (network processing vertically integrated seismic analysis) and is designed to replace the current automated network processing at the IDC, the SEL3 bulletin. Our results (attached table) demonstrate that NET-VISA significantly outperforms SEL3 by reducing the missed events from 30.3% down to 12.5%. The difference is even more dramatic for smaller magnitude events. NET-VISA has no difficulty in locating nuclear explosions as well. The attached figure demonstrates the location predicted by NET-VISA versus other bulletins for the second DPRK event. Further evaluation on dense regional networks demonstrates that NET-VISA finds many events missed in the LEB bulletin, which is produced by the human analysts. Large aftershock sequences, as produced by the 2004 December Sumatra earthquake and the 2011 March Tohoku earthquake, can pose a significant load for automated processing, often delaying the IDC bulletins by weeks or months. Indeed these sequences can overload the serial NET-VISA inference as well. We describe an enhancement to NET-VISA to make it multi-threaded, and hence take full advantage of the processing power of multi-core and -cpu machines. Our experiments show that the new inference algorithm is able to achieve 80% efficiency in parallel speedup.

  3. Maximum caliber inference of nonequilibrium processes.

    PubMed

    Otten, Moritz; Stock, Gerhard

    2010-07-21

    Thirty years ago, Jaynes suggested a general theoretical approach to nonequilibrium statistical mechanics, called maximum caliber (MaxCal) [Annu. Rev. Phys. Chem. 31, 579 (1980)]. MaxCal is a variational principle for dynamics in the same spirit that maximum entropy is a variational principle for equilibrium statistical mechanics. Motivated by the success of maximum entropy inference methods for equilibrium problems, in this work the MaxCal formulation is applied to the inference of nonequilibrium processes. That is, given some time-dependent observables of a dynamical process, one constructs a model that reproduces these input data and moreover, predicts the underlying dynamics of the system. For example, the observables could be some time-resolved measurements of the folding of a protein, which are described by a few-state model of the free energy landscape of the system. MaxCal then calculates the probabilities of an ensemble of trajectories such that on average the data are reproduced. From this probability distribution, any dynamical quantity of the system can be calculated, including population probabilities, fluxes, or waiting time distributions. After briefly reviewing the formalism, the practical numerical implementation of MaxCal in the case of an inference problem is discussed. Adopting various few-state models of increasing complexity, it is demonstrated that the MaxCal principle indeed works as a practical method of inference: The scheme is fairly robust and yields correct results as long as the input data are sufficient. As the method is unbiased and general, it can deal with any kind of time dependency such as oscillatory transients and multitime decays. PMID:20649320

  4. Mitochondrial deficiency in Cockayne syndrome

    PubMed Central

    Scheibye-Knudsen, Morten; Croteau, Deborah L.; Bohr, Vilhelm A.

    2013-01-01

    Cockayne syndrome is a rare inherited disorder characterized by accelerated aging, cachectic dwarfism and many other features. Recent work has implicated mitochondrial dysfunction in the pathogenesis of this disease. This is particularly interesting since mitochondrial deficiencies are believed to be important in the aging process. In this review, we will discuss recent findings of mitochondrial pathology in Cockayne syndrome and suggest possible mechanisms for the mitochondrial dysfunction. PMID:23435289

  5. Predictive Bayesian inference and dynamic treatment regimes.

    PubMed

    Saarela, Olli; Arjas, Elja; Stephens, David A; Moodie, Erica E M

    2015-11-01

    While optimal dynamic treatment regimes (DTRs) can be estimated without specification of a predictive model, a model-based approach, combined with dynamic programming and Monte Carlo integration, enables direct probabilistic comparisons between the outcomes under the optimal DTR and alternative (dynamic or static) treatment regimes. The Bayesian predictive approach also circumvents problems related to frequentist estimators under the nonregular estimation problem. However, the model-based approach is susceptible to misspecification, in particular of the "null-paradox" type, which is due to the model parameters not having a direct causal interpretation in the presence of latent individual-level characteristics. Because it is reasonable to insist on correct inferences under the null of no difference between the alternative treatment regimes, we discuss how to achieve this through a "null-robust" reparametrization of the problem in a longitudinal setting. Since we argue that causal inference can be entirely understood as posterior predictive inference in a hypothetical population without covariate imbalances, we also discuss how controlling for confounding through inverse probability of treatment weighting can be justified and incorporated in the Bayesian setting. PMID:26259996

  6. Inferring Epidemic Network Topology from Surveillance Data

    PubMed Central

    Wan, Xiang; Liu, Jiming; Cheung, William K.; Tong, Tiejun

    2014-01-01

    The transmission of infectious diseases can be affected by many or even hidden factors, making it difficult to accurately predict when and where outbreaks may emerge. One approach at the moment is to develop and deploy surveillance systems in an effort to detect outbreaks as timely as possible. This enables policy makers to modify and implement strategies for the control of the transmission. The accumulated surveillance data including temporal, spatial, clinical, and demographic information, can provide valuable information with which to infer the underlying epidemic networks. Such networks can be quite informative and insightful as they characterize how infectious diseases transmit from one location to another. The aim of this work is to develop a computational model that allows inferences to be made regarding epidemic network topology in heterogeneous populations. We apply our model on the surveillance data from the 2009 H1N1 pandemic in Hong Kong. The inferred epidemic network displays significant effect on the propagation of infectious diseases. PMID:24979215

  7. Quality of Computationally Inferred Gene Ontology Annotations

    PubMed Central

    Škunca, Nives; Altenhoff, Adrian; Dessimoz, Christophe

    2012-01-01

    Gene Ontology (GO) has established itself as the undisputed standard for protein function annotation. Most annotations are inferred electronically, i.e. without individual curator supervision, but they are widely considered unreliable. At the same time, we crucially depend on those automated annotations, as most newly sequenced genomes are non-model organisms. Here, we introduce a methodology to systematically and quantitatively evaluate electronic annotations. By exploiting changes in successive releases of the UniProt Gene Ontology Annotation database, we assessed the quality of electronic annotations in terms of specificity, reliability, and coverage. Overall, we not only found that electronic annotations have significantly improved in recent years, but also that their reliability now rivals that of annotations inferred by curators when they use evidence other than experiments from primary literature. This work provides the means to identify the subset of electronic annotations that can be relied upon—an important outcome given that >98% of all annotations are inferred without direct curation. PMID:22693439

  8. Variational Inference for Watson Mixture Model.

    PubMed

    Taghia, Jalil; Leijon, Arne

    2016-09-01

    This paper addresses modelling data using the Watson distribution. The Watson distribution is one of the simplest distributions for analyzing axially symmetric data. This distribution has gained some attention in recent years due to its modeling capability. However, its Bayesian inference is fairly understudied due to difficulty in handling the normalization factor. Recent development of Markov chain Monte Carlo (MCMC) sampling methods can be applied for this purpose. However, these methods can be prohibitively slow for practical applications. A deterministic alternative is provided by variational methods that convert inference problems into optimization problems. In this paper, we present a variational inference for Watson mixture models. First, the variational framework is used to side-step the intractability arising from the coupling of latent states and parameters. Second, the variational free energy is further lower bounded in order to avoid intractable moment computation. The proposed approach provides a lower bound on the log marginal likelihood and retains distributional information over all parameters. Moreover, we show that it can regulate its own complexity by pruning unnecessary mixture components while avoiding over-fitting. We discuss potential applications of the modeling with Watson distributions in the problem of blind source separation, and clustering gene expression data sets. PMID:26571512

  9. Optical tweezers calibration with Bayesian inference

    NASA Astrophysics Data System (ADS)

    Türkcan, Silvan; Richly, Maximilian U.; Le Gall, Antoine; Fiszman, Nicolas; Masson, Jean-Baptiste; Westbrook, Nathalie; Perronet, Karen; Alexandrou, Antigoni

    2014-09-01

    We present a new method for calibrating an optical-tweezer setup that is based on Bayesian inference1. This method employs an algorithm previously used to analyze the confined trajectories of receptors within lipid rafts2,3. The main advantages of this method are that it does not require input parameters and is insensitive to systematic errors like the drift of the setup. Additionally, it exploits a much larger amount of the information stored in the recorded bead trajectory than standard calibration approaches. The additional information can be used to detect deviations from the perfect harmonic potential or detect environmental influences on the bead. The algorithm infers the diffusion coefficient and the potential felt by a trapped bead, and only requires the bead trajectory as input. We demonstrate that this method outperforms the equipartition method and the power-spectrum method in input information required (bead radius and trajectory length) and in output accuracy. Furthermore, by inferring a higher order potential our method can reveal deviations from the assumed second-order potential. More generally, this method can also be used for magnetic-tweezer calibration.

  10. Inferring sparse networks for noisy transient processes.

    PubMed

    Tran, Hoang M; Bukkapatnam, Satish T S

    2016-01-01

    Inferring causal structures of real world complex networks from measured time series signals remains an open issue. The current approaches are inadequate to discern between direct versus indirect influences (i.e., the presence or absence of a directed arc connecting two nodes) in the presence of noise, sparse interactions, as well as nonlinear and transient dynamics of real world processes. We report a sparse regression (referred to as the l1-min) approach with theoretical bounds on the constraints on the allowable perturbation to recover the network structure that guarantees sparsity and robustness to noise. We also introduce averaging and perturbation procedures to further enhance prediction scores (i.e., reduce inference errors), and the numerical stability of l1-min approach. Extensive investigations have been conducted with multiple benchmark simulated genetic regulatory network and Michaelis-Menten dynamics, as well as real world data sets from DREAM5 challenge. These investigations suggest that our approach can significantly improve, oftentimes by 5 orders of magnitude over the methods reported previously for inferring the structure of dynamic networks, such as Bayesian network, network deconvolution, silencing and modular response analysis methods based on optimizing for sparsity, transients, noise and high dimensionality issues. PMID:26916813

  11. Inferring identify from DNA profile evidence.

    PubMed

    Balding, D J; Donnelly, P

    1995-12-01

    The controversy over the interpretation of DNA profile evidence in forensic identification can be attributed in part to confusion over the mode(s) of statistical inference appropriate to this setting. Although there has been substantial discussion in the literature of, for example, the role of population genetics issues, few authors have made explicit the inferential framework which underpins their arguments. This lack of clarity has led both to unnecessary debates over ill-posed or inappropriate questions and to the neglect of some issues which can have important consequences. We argue that the mode of statistical inference which seems to underlie the arguments of some authors, based on a hypothesis testing framework, is not appropriate for forensic identification. We propose instead a logically coherent framework in which, for example, the roles both of the population genetics issues and of the nonscientific evidence in a case are incorporated. Our analysis highlights several widely held misconceptions in the DNA profiling debate. For example, the profile frequency is not directly relevant to forensic inference. Further, very small match probabilities may in some settings be consistent with acquittal. Although DNA evidence is typically very strong, our analysis of the coherent approach highlights situations which can arise in practice where alternative methods for assessing DNA evidence may be misleading. PMID:8524840

  12. Inferred Lunar Boulder Distributions at Decimeter Scales

    NASA Technical Reports Server (NTRS)

    Baloga, S. M.; Glaze, L. S.; Spudis, P. D.

    2012-01-01

    Block size distributions of impact deposits on the Moon are diagnostic of the impact process and environmental effects, such as target lithology and weathering. Block size distributions are also important factors in trafficability, habitability, and possibly the identification of indigenous resources. Lunar block sizes have been investigated for many years for many purposes [e.g., 1-3]. An unresolved issue is the extent to which lunar block size distributions can be extrapolated to scales smaller than limits of resolution of direct measurement. This would seem to be a straightforward statistical application, but it is complicated by two issues. First, the cumulative size frequency distribution of observable boulders rolls over due to resolution limitations at the small end. Second, statistical regression provides the best fit only around the centroid of the data [4]. Confidence and prediction limits splay away from the best fit at the endpoints resulting in inferences in the boulder density at the CPR scale that can differ by many orders of magnitude [4]. These issues were originally investigated by Cintala and McBride [2] using Surveyor data. The objective of this study was to determine whether the measured block size distributions from Lunar Reconnaissance Orbiter Camera - Narrow Angle Camera (LROC-NAC) images (m-scale resolution) can be used to infer the block size distribution at length scales comparable to Mini-RF Circular Polarization Ratio (CPR) scales, nominally taken as 10 cm. This would set the stage for assessing correlations of inferred block size distributions with CPR returns [6].

  13. Is There a Free Lunch in Inference?

    PubMed

    Rouder, Jeffrey N; Morey, Richard D; Verhagen, Josine; Province, Jordan M; Wagenmakers, Eric-Jan

    2016-07-01

    The field of psychology, including cognitive science, is vexed by a crisis of confidence. Although the causes and solutions are varied, we focus here on a common logical problem in inference. The default mode of inference is significance testing, which has a free lunch property where researchers need not make detailed assumptions about the alternative to test the null hypothesis. We present the argument that there is no free lunch; that is, valid testing requires that researchers test the null against a well-specified alternative. We show how this requirement follows from the basic tenets of conventional and Bayesian probability. Moreover, we show in both the conventional and Bayesian framework that not specifying the alternative may lead to rejections of the null hypothesis with scant evidence. We review both frequentist and Bayesian approaches to specifying alternatives, and we show how such specifications improve inference. The field of cognitive science will benefit because consideration of reasonable alternatives will undoubtedly sharpen the intellectual underpinnings of research. PMID:27489199

  14. Evolutionary inferences from the analysis of exchangeability

    PubMed Central

    Hendry, Andrew P.; Kaeuffer, Renaud; Crispo, Erika; Peichel, Catherine L.; Bolnick, Daniel I.

    2013-01-01

    Evolutionary inferences are usually based on statistical models that compare mean genotypes and phenotypes (or their frequencies) among populations. An alternative is to use the actual distribution of genotypes and phenotypes to infer the “exchangeability” of individuals among populations. We illustrate this approach by using discriminant functions on principal components to classify individuals among paired lake and stream populations of threespine stickleback in each of six independent watersheds. Classification based on neutral and non-neutral microsatellite markers was highest to the population of origin and next-highest to populations in the same watershed. These patterns are consistent with the influence of historical contingency (separate colonization of each watershed) and subsequent gene flow (within but not between watersheds). In comparison to this low genetic exchangeability, ecological (diet) and morphological (trophic and armor traits) exchangeability was relatively high – particularly among populations from similar habitats. These patterns reflect the role of natural selection in driving parallel changes adaptive changes when independent populations colonize similar habitats. Importantly, however, substantial non-parallelism was also evident. Our results show that analyses based on exchangeability can confirm inferences based on statistical analyses of means or frequencies, while also refining insights into the drivers of – and constraints on – evolutionary diversification. PMID:24299398

  15. Inferring sparse networks for noisy transient processes

    NASA Astrophysics Data System (ADS)

    Tran, Hoang M.; Bukkapatnam, Satish T. S.

    2016-02-01

    Inferring causal structures of real world complex networks from measured time series signals remains an open issue. The current approaches are inadequate to discern between direct versus indirect influences (i.e., the presence or absence of a directed arc connecting two nodes) in the presence of noise, sparse interactions, as well as nonlinear and transient dynamics of real world processes. We report a sparse regression (referred to as the -min) approach with theoretical bounds on the constraints on the allowable perturbation to recover the network structure that guarantees sparsity and robustness to noise. We also introduce averaging and perturbation procedures to further enhance prediction scores (i.e., reduce inference errors), and the numerical stability of -min approach. Extensive investigations have been conducted with multiple benchmark simulated genetic regulatory network and Michaelis-Menten dynamics, as well as real world data sets from DREAM5 challenge. These investigations suggest that our approach can significantly improve, oftentimes by 5 orders of magnitude over the methods reported previously for inferring the structure of dynamic networks, such as Bayesian network, network deconvolution, silencing and modular response analysis methods based on optimizing for sparsity, transients, noise and high dimensionality issues.

  16. Inferring sparse networks for noisy transient processes

    PubMed Central

    Tran, Hoang M.; Bukkapatnam, Satish T.S.

    2016-01-01

    Inferring causal structures of real world complex networks from measured time series signals remains an open issue. The current approaches are inadequate to discern between direct versus indirect influences (i.e., the presence or absence of a directed arc connecting two nodes) in the presence of noise, sparse interactions, as well as nonlinear and transient dynamics of real world processes. We report a sparse regression (referred to as the -min) approach with theoretical bounds on the constraints on the allowable perturbation to recover the network structure that guarantees sparsity and robustness to noise. We also introduce averaging and perturbation procedures to further enhance prediction scores (i.e., reduce inference errors), and the numerical stability of -min approach. Extensive investigations have been conducted with multiple benchmark simulated genetic regulatory network and Michaelis-Menten dynamics, as well as real world data sets from DREAM5 challenge. These investigations suggest that our approach can significantly improve, oftentimes by 5 orders of magnitude over the methods reported previously for inferring the structure of dynamic networks, such as Bayesian network, network deconvolution, silencing and modular response analysis methods based on optimizing for sparsity, transients, noise and high dimensionality issues. PMID:26916813

  17. Inferring Pedigree Graphs from Genetic Distances

    NASA Astrophysics Data System (ADS)

    Tamura, Takeyuki; Ito, Hiro

    In this paper, we study a problem of inferring blood relationships which satisfy a given matrix of genetic distances between all pairs of n nodes. Blood relationships are represented by our proposed graph class, which is called a pedigree graph. A pedigree graph is a directed acyclic graph in which the maximum indegree is at most two. We show that the number of pedigree graphs which satisfy the condition of given genetic distances may be exponential, but they can be represented by one directed acyclic graph with n nodes. Moreover, an O(n3) time algorithm which solves the problem is also given. Although phylogenetic trees and phylogenetic networks are similar data structures to pedigree graphs, it seems that inferring methods for phylogenetic trees and networks cannot be applied to infer pedigree graphs since nodes of phylogenetic trees and networks represent species whereas nodes of pedigree graphs represent individuals. We also show an O(n2) time algorithm which detects a contradiction between a given pedigreee graph and distance matrix of genetic distances.

  18. Functional neuroanatomy of intuitive physical inference.

    PubMed

    Fischer, Jason; Mikhael, John G; Tenenbaum, Joshua B; Kanwisher, Nancy

    2016-08-23

    To engage with the world-to understand the scene in front of us, plan actions, and predict what will happen next-we must have an intuitive grasp of the world's physical structure and dynamics. How do the objects in front of us rest on and support each other, how much force would be required to move them, and how will they behave when they fall, roll, or collide? Despite the centrality of physical inferences in daily life, little is known about the brain mechanisms recruited to interpret the physical structure of a scene and predict how physical events will unfold. Here, in a series of fMRI experiments, we identified a set of cortical regions that are selectively engaged when people watch and predict the unfolding of physical events-a "physics engine" in the brain. These brain regions are selective to physical inferences relative to nonphysical but otherwise highly similar scenes and tasks. However, these regions are not exclusively engaged in physical inferences per se or, indeed, even in scene understanding; they overlap with the domain-general "multiple demand" system, especially the parts of that system involved in action planning and tool use, pointing to a close relationship between the cognitive and neural mechanisms involved in parsing the physical content of a scene and preparing an appropriate action. PMID:27503892

  19. Combinatorics of distance-based tree inference.

    PubMed

    Pardi, Fabio; Gascuel, Olivier

    2012-10-01

    Several popular methods for phylogenetic inference (or hierarchical clustering) are based on a matrix of pairwise distances between taxa (or any kind of objects): The objective is to construct a tree with branch lengths so that the distances between the leaves in that tree are as close as possible to the input distances. If we hold the structure (topology) of the tree fixed, in some relevant cases (e.g., ordinary least squares) the optimal values for the branch lengths can be expressed using simple combinatorial formulae. Here we define a general form for these formulae and show that they all have two desirable properties: First, the common tree reconstruction approaches (least squares, minimum evolution), when used in combination with these formulae, are guaranteed to infer the correct tree when given enough data (consistency); second, the branch lengths of all the simple (nearest neighbor interchange) rearrangements of a tree can be calculated, optimally, in quadratic time in the size of the tree, thus allowing the efficient application of hill climbing heuristics. The study presented here is a continuation of that by Mihaescu and Pachter on branch length estimation [Mihaescu R, Pachter L (2008) Proc Natl Acad Sci USA 105:13206-13211]. The focus here is on the inference of the tree itself and on providing a basis for novel algorithms to reconstruct trees from distances. PMID:23012403

  20. Combinatorics of distance-based tree inference

    PubMed Central

    Pardi, Fabio; Gascuel, Olivier

    2012-01-01

    Several popular methods for phylogenetic inference (or hierarchical clustering) are based on a matrix of pairwise distances between taxa (or any kind of objects): The objective is to construct a tree with branch lengths so that the distances between the leaves in that tree are as close as possible to the input distances. If we hold the structure (topology) of the tree fixed, in some relevant cases (e.g., ordinary least squares) the optimal values for the branch lengths can be expressed using simple combinatorial formulae. Here we define a general form for these formulae and show that they all have two desirable properties: First, the common tree reconstruction approaches (least squares, minimum evolution), when used in combination with these formulae, are guaranteed to infer the correct tree when given enough data (consistency); second, the branch lengths of all the simple (nearest neighbor interchange) rearrangements of a tree can be calculated, optimally, in quadratic time in the size of the tree, thus allowing the efficient application of hill climbing heuristics. The study presented here is a continuation of that by Mihaescu and Pachter on branch length estimation [Mihaescu R, Pachter L (2008) Proc Natl Acad Sci USA 105:13206–13211]. The focus here is on the inference of the tree itself and on providing a basis for novel algorithms to reconstruct trees from distances. PMID:23012403

  1. Multiple Peroxisomal Enzymatic Deficiency Disorders

    PubMed Central

    Vamecq, Joseph; Draye, Jean-Pierre; Van Hoof, François; Misson, Jean-Paul; Evrard, Philippe; Verellen, Gaston; Eyssen, Hendrik J.; Van Eldere, Johan; Schutgens, Ruud B. H.; Wanders, Ronald J. A.; Roels, Frank; Goldfischer, Sidney L.

    1986-01-01

    Biologic, morphologic, and biochemical investigations performed in 2 patients demonstrate multiple peroxisomal deficiencies in the cerebrohepatorenal syndrome of Zellweger (CHRS) and neonatal adrenoleukodystrophy (NALD). Very long chain fatty acids, abnormal bile acids, including bile acid precursors (di- and trihydroxycoprostanoic acids), and C29-dicarboxylic acid accumulated in plasma in both patients. Generalized hyperaminoaciduria was also present. Peroxisomes could not be detected in CHRS liver and kidney; however, in the NALD patient, small and sparse cytoplasmic bodies resembling altered peroxisomes were found in hepatocytes. Hepatocellular and Kupffer cell lysosomes were engorged with ferritin and contained clefts and trilaminar structures believed to represent very long chain fatty acids. Enzymatic deficiencies reflected the peroxisomal defects. Hepatic glycolate oxidase and palmitoyl-CoA oxidase activities were deficient. No particle-bound catalase was found in cultured fibroblasts, and ether glycerolipid (plasmalogen) biosynthesis was markedly reduced. Administration of phenobarbital and clofibrate, an agent that induces peroxisomal proliferation and enzymatic activities, to the NALD patient did not bring about any changes in plasma metabolites, liver peroxisome population, or oxidizing activities. ImagesFigure 1Figure 2Figure 3Figure 4Figure 5 PMID:2879480

  2. Functional consequences of zinc deficiency.

    PubMed

    McClain, C J; Kasarskis, E J; Allen, J J

    1985-01-01

    Zinc is an essential trace element necessary for over 200 zinc metalloenzymes and required for normal nucleic acid, protein, and membrane metabolism. During the past two decades there has been a rapid expansion of knowledge concerning zinc metabolism in both normal and disease situations, including mechanisms for zinc absorption, excretion and internal redistribution of zinc after stress or trauma. Acrodermatitis enteropathica has been recognized to be a disease of impaired zinc absorption in man. A host of disease processes now are recognized to be complicated by zinc deficiency including alcoholic liver disease, sickle cell anemia, protein calorie malnutrition, and a variety of intestinal diseases including Crohn's disease, sprue, short bowel syndrome and after jejunal ileal bypass. Zinc has proved to be an extremely interesting mineral to nutritionists and physicians because of its importance in normal physiology and biochemistry and because of the diverse presenting features of zinc deficiency. This paper reviews ten functional consequences of zinc deficiency and emphasizes certain consequences in which there have been new discoveries concerning their mechanism (e.g., anorexia) or their clinical importance (e.g., immune dysfunction). PMID:3911268

  3. Vitamin D recommendations: beyond deficiency.

    PubMed

    Biesalski, Hans K

    2011-01-01

    Vitamin D plays an important role in regular bone growth and in adequate function of the innate immune system, including barrier functions of mucous membranes. A sufficient supply during pregnancy and lactation protects the child from infectious diseases. Clinical symptoms of severe vitamin D deficiency (rickets) are well known and can be easily detected. Signs and symptoms beyond deficiency, however, remain to be elucidated. Based on clinical and observational data, the plasma level of 25(OH)D may serve as a 'marker' to detect or define a subclinical deficiency. Levels below 50 nmol/l might be insufficient to maintain the non-bone-related activities of vitamin D. Finally, it has to be considered that all of the nonbone activities of vitamin D are in concert with vitamin A (9-cis retinoic acid). Studies combining both vitamins in sufficient amounts (cod liver oil) demonstrated a beneficial effect on the prevention of respiratory tract infections. Consequently, it should be strongly recommended to increase the intake of vitamin D and to ensure a daily intake of vitamin A as counseled. PMID:22123631

  4. Mitochondrial Cytochrome c Oxidase Deficiency

    PubMed Central

    Rak, Malgorzata; Bénit, Paule; Chrétien, Dominique; Bouchereau, Juliette; Schiff, Manuel; El-Khoury, Riyad; Tzagoloff, Alexander; Rustin, Pierre

    2016-01-01

    As with other mitochondrial respiratory chain components, marked clinical and genetic heterogeneity is observed in patients with a cytochrome c oxidase deficiency. This constitutes a considerable diagnostic challenge and raises a number of puzzling questions. So far, pathological mutations have been reported in more than 30 genes, in both mitochondrial and nuclear DNA, affecting either structural subunits of the enzyme or proteins involved in its biogenesis. In this review, we discuss the possible causes of the discrepancy between the spectacular advances made in the identification of the molecular bases of cytochrome oxidase deficiency and the lack of any efficient treatment in diseases resulting from such deficiencies. This brings back many unsolved questions related to the frequent delay of clinical manifestation, variable course and severity, and tissue-involvement often associated with these diseases. In this context, we stress the importance to study different models of these diseases, but also discuss the limitations encountered in most available disease models. In the future, with the possible exception of replacement therapy using genes, cells or organs, a better understanding of underlying mechanism(s) of these mitochondrial diseases is presumably required to develop efficient therapy. PMID:26846578

  5. The Meniscus-Deficient Knee

    PubMed Central

    Rao, Allison J.; Erickson, Brandon J.; Cvetanovich, Gregory L.; Yanke, Adam B.; Bach, Bernard R.; Cole, Brian J.

    2015-01-01

    Meniscal tears are the most common knee injury, and partial meniscectomies are the most common orthopaedic surgical procedure. The injured meniscus has an impaired ability to distribute load and resist tibial translation. Partial or complete loss of the meniscus promotes early development of chondromalacia and osteoarthritis. The primary goal of treatment for meniscus-deficient knees is to provide symptomatic relief, ideally to delay advanced joint space narrowing, and ultimately, joint replacement. Surgical treatments, including meniscal allograft transplantation (MAT), high tibial osteotomy (HTO), and distal femoral osteotomy (DFO), are options that attempt to decrease the loads on the articular cartilage of the meniscus-deficient compartment by replacing meniscal tissue or altering joint alignment. Clinical and biomechanical studies have reported promising outcomes for MAT, HTO, and DFO in the postmeniscectomized knee. These procedures can be performed alone or in conjunction with ligament reconstruction or chondral procedures (reparative, restorative, or reconstructive) to optimize stability and longevity of the knee. Complications can include fracture, nonunion, patella baja, compartment syndrome, infection, and deep venous thrombosis. MAT, HTO, and DFO are effective options for young patients suffering from pain and functional limitations secondary to meniscal deficiency. PMID:26779547

  6. Nutritional Deficiencies and Phospholipid Metabolism

    PubMed Central

    Gimenez, María S.; Oliveros, Liliana B.; Gomez, Nidia N.

    2011-01-01

    Phospholipids are important components of the cell membranes of all living species. They contribute to the physicochemical properties of the membrane and thus influence the conformation and function of membrane-bound proteins, such as receptors, ion channels, and transporters and also influence cell function by serving as precursors for prostaglandins and other signaling molecules and modulating gene expression through the transcription activation. The components of the diet are determinant for cell functionality. In this review, the effects of macro and micronutrients deficiency on the quality, quantity and metabolism of different phospholipids and their distribution in cells of different organs is presented. Alterations in the amount of both saturated and polyunsaturated fatty acids, vitamins A, E and folate, and other micronutrients, such as zinc and magnesium, are discussed. In all cases we observe alterations in the pattern of phospholipids, the more affected ones being phosphatidylcholine, phosphatidylethanolamine and sphingomyelin. The deficiency of certain nutrients, such as essential fatty acids, fat-soluble vitamins and some metals may contribute to a variety of diseases that can be irreversible even after replacement with normal amount of the nutrients. Usually, the sequelae are more important when the deficiency is present at an early age. PMID:21731449

  7. Flu Vaccine Guidance for Patients with Immune Deficiency

    MedlinePlus

    ... Guidance for Patients with Immune Deficiency Share | Flu Vaccine Guidance for Patients with Immune Deficiency This article ... should patients with immune deficiency be given the vaccine? Immune deficient patients have a decreased resistance to ...

  8. Iodine deficiency disorders (IDD) and their eradication.

    PubMed

    Hetzel, B S

    1983-11-12

    Disorders resulting from severe iodine deficiency affect more than 400 million people in Asia alone. These disorders include stillbirths, abortions, and congenital anomalies; endemic cretinism, characterised most commonly by mental deficiency, deaf mutism, and spastic diplegia and lesser degrees of neurological defect related to fetal iodine deficiency; and impaired mental function in children and adults with goitre associated with subnormal concentrations of circulating thyroxine. Use of the term iodine deficiency disorders, instead of "goitre", would help to bridge the serious gap between knowledge and its application. Iodised salt and iodised oil (by injection or by mouth) are suitable for the correction of iodine deficiency on a mass scale. A single dose of iodised oil can correct severe iodine deficiency for 3-5 years. Iodised oil offers a satisfactory immediate measure for primary care services until an iodised salt programme can be implemented. The complete eradication of iodine deficiency is therefore feasible within 5-10 years. PMID:6138653

  9. Statistical Inference at Work: Statistical Process Control as an Example

    ERIC Educational Resources Information Center

    Bakker, Arthur; Kent, Phillip; Derry, Jan; Noss, Richard; Hoyles, Celia

    2008-01-01

    To characterise statistical inference in the workplace this paper compares a prototypical type of statistical inference at work, statistical process control (SPC), with a type of statistical inference that is better known in educational settings, hypothesis testing. Although there are some similarities between the reasoning structure involved in…

  10. Development of L2 Word-Meaning Inference while Reading

    ERIC Educational Resources Information Center

    Hamada, Megumi

    2009-01-01

    Ability to infer the meaning of unknown words encountered while reading plays an important role in learners' L2 word-knowledge development. Despite numerous findings reported on word-meaning inference, how learners develop this ability is still unclear. In order to provide a developmental inquiry into L2 word-meaning inference while reading, this…

  11. Deficiencies in the Management of Iron Deficiency Anemia During Childhood.

    PubMed

    Powers, Jacquelyn M; Daniel, Catherine L; McCavit, Timothy L; Buchanan, George R

    2016-04-01

    Limited high-quality evidence supports the management of iron deficiency anemia (IDA). To assess our institutional performance in this area, we retrospectively reviewed IDA treatment practices in 195 consecutive children referred to our center from 2006 to mid-2010. The majority of children were ≤4 years old (64%) and had nutritional IDA (74%). In 11- to 18-year-old patients (31%), the primary etiology was menorrhagia (42%). Many were referred directly to the emergency department and/or prescribed iron doses outside the recommended range. Poor medication adherence and being lost-to-follow-up were common. Substantial improvements are required in the management of IDA. PMID:26728130

  12. Inferring epidemiological dynamics with Bayesian coalescent inference: the merits of deterministic and stochastic models.

    PubMed

    Popinga, Alex; Vaughan, Tim; Stadler, Tanja; Drummond, Alexei J

    2015-02-01

    Estimation of epidemiological and population parameters from molecular sequence data has become central to the understanding of infectious disease dynamics. Various models have been proposed to infer details of the dynamics that describe epidemic progression. These include inference approaches derived from Kingman's coalescent theory. Here, we use recently described coalescent theory for epidemic dynamics to develop stochastic and deterministic coalescent susceptible-infected-removed (SIR) tree priors. We implement these in a Bayesian phylogenetic inference framework to permit joint estimation of SIR epidemic parameters and the sample genealogy. We assess the performance of the two coalescent models and also juxtapose results obtained with a recently published birth-death-sampling model for epidemic inference. Comparisons are made by analyzing sets of genealogies simulated under precisely known epidemiological parameters. Additionally, we analyze influenza A (H1N1) sequence data sampled in the Canterbury region of New Zealand and HIV-1 sequence data obtained from known United Kingdom infection clusters. We show that both coalescent SIR models are effective at estimating epidemiological parameters from data with large fundamental reproductive number [Formula: see text] and large population size [Formula: see text]. Furthermore, we find that the stochastic variant generally outperforms its deterministic counterpart in terms of error, bias, and highest posterior density coverage, particularly for smaller [Formula: see text] and [Formula: see text]. However, each of these inference models is shown to have undesirable properties in certain circumstances, especially for epidemic outbreaks with [Formula: see text] close to one or with small effective susceptible populations. PMID:25527289

  13. Inferring influenza dynamics and control in households.

    PubMed

    Lau, Max S Y; Cowling, Benjamin J; Cook, Alex R; Riley, Steven

    2015-07-21

    Household-based interventions are the mainstay of public health policy against epidemic respiratory pathogens when vaccination is not available. Although the efficacy of these interventions has traditionally been measured by their ability to reduce the proportion of household contacts who exhibit symptoms [household secondary attack rate (hSAR)], this metric is difficult to interpret and makes only partial use of data collected by modern field studies. Here, we use Bayesian transmission model inference to analyze jointly both symptom reporting and viral shedding data from a three-armed study of influenza interventions. The reduction in hazard of infection in the increased hand hygiene intervention arm was 37.0% [8.3%, 57.8%], whereas the equivalent reduction in the other intervention arm was 27.2% [-0.46%, 52.3%] (increased hand hygiene and face masks). By imputing the presence and timing of unobserved infection, we estimated that only 61.7% [43.1%, 76.9%] of infections met the case criteria and were thus detected by the study design. An assessment of interventions using inferred infections produced more intuitively consistent attack rates when households were stratified by the speed of intervention, compared with the crude hSAR. Compared with adults, children were 2.29 [1.66, 3.23] times as infectious and 3.36 [2.31, 4.82] times as susceptible. The mean generation time was 3.39 d [3.06, 3.70]. Laboratory confirmation of infections by RT-PCR was only able to detect 79.6% [76.5%, 83.0%] of symptomatic infections, even at the peak of shedding. Our results highlight the potential use of robust inference with well-designed mechanistic transmission models to improve the design of intervention studies. PMID:26150502

  14. Bayesian Estimation and Inference Using Stochastic Electronics

    PubMed Central

    Thakur, Chetan Singh; Afshar, Saeed; Wang, Runchun M.; Hamilton, Tara J.; Tapson, Jonathan; van Schaik, André

    2016-01-01

    In this paper, we present the implementation of two types of Bayesian inference problems to demonstrate the potential of building probabilistic algorithms in hardware using single set of building blocks with the ability to perform these computations in real time. The first implementation, referred to as the BEAST (Bayesian Estimation and Stochastic Tracker), demonstrates a simple problem where an observer uses an underlying Hidden Markov Model (HMM) to track a target in one dimension. In this implementation, sensors make noisy observations of the target position at discrete time steps. The tracker learns the transition model for target movement, and the observation model for the noisy sensors, and uses these to estimate the target position by solving the Bayesian recursive equation online. We show the tracking performance of the system and demonstrate how it can learn the observation model, the transition model, and the external distractor (noise) probability interfering with the observations. In the second implementation, referred to as the Bayesian INference in DAG (BIND), we show how inference can be performed in a Directed Acyclic Graph (DAG) using stochastic circuits. We show how these building blocks can be easily implemented using simple digital logic gates. An advantage of the stochastic electronic implementation is that it is robust to certain types of noise, which may become an issue in integrated circuit (IC) technology with feature sizes in the order of tens of nanometers due to their low noise margin, the effect of high-energy cosmic rays and the low supply voltage. In our framework, the flipping of random individual bits would not affect the system performance because information is encoded in a bit stream. PMID:27047326

  15. Nonparametric inference of network structure and dynamics

    NASA Astrophysics Data System (ADS)

    Peixoto, Tiago P.

    The network structure of complex systems determine their function and serve as evidence for the evolutionary mechanisms that lie behind them. Despite considerable effort in recent years, it remains an open challenge to formulate general descriptions of the large-scale structure of network systems, and how to reliably extract such information from data. Although many approaches have been proposed, few methods attempt to gauge the statistical significance of the uncovered structures, and hence the majority cannot reliably separate actual structure from stochastic fluctuations. Due to the sheer size and high-dimensionality of many networks, this represents a major limitation that prevents meaningful interpretations of the results obtained with such nonstatistical methods. In this talk, I will show how these issues can be tackled in a principled and efficient fashion by formulating appropriate generative models of network structure that can have their parameters inferred from data. By employing a Bayesian description of such models, the inference can be performed in a nonparametric fashion, that does not require any a priori knowledge or ad hoc assumptions about the data. I will show how this approach can be used to perform model comparison, and how hierarchical models yield the most appropriate trade-off between model complexity and quality of fit based on the statistical evidence present in the data. I will also show how this general approach can be elegantly extended to networks with edge attributes, that are embedded in latent spaces, and that change in time. The latter is obtained via a fully dynamic generative network model, based on arbitrary-order Markov chains, that can also be inferred in a nonparametric fashion. Throughout the talk I will illustrate the application of the methods with many empirical networks such as the internet at the autonomous systems level, the global airport network, the network of actors and films, social networks, citations among

  16. Bayesian Estimation and Inference Using Stochastic Electronics.

    PubMed

    Thakur, Chetan Singh; Afshar, Saeed; Wang, Runchun M; Hamilton, Tara J; Tapson, Jonathan; van Schaik, André

    2016-01-01

    In this paper, we present the implementation of two types of Bayesian inference problems to demonstrate the potential of building probabilistic algorithms in hardware using single set of building blocks with the ability to perform these computations in real time. The first implementation, referred to as the BEAST (Bayesian Estimation and Stochastic Tracker), demonstrates a simple problem where an observer uses an underlying Hidden Markov Model (HMM) to track a target in one dimension. In this implementation, sensors make noisy observations of the target position at discrete time steps. The tracker learns the transition model for target movement, and the observation model for the noisy sensors, and uses these to estimate the target position by solving the Bayesian recursive equation online. We show the tracking performance of the system and demonstrate how it can learn the observation model, the transition model, and the external distractor (noise) probability interfering with the observations. In the second implementation, referred to as the Bayesian INference in DAG (BIND), we show how inference can be performed in a Directed Acyclic Graph (DAG) using stochastic circuits. We show how these building blocks can be easily implemented using simple digital logic gates. An advantage of the stochastic electronic implementation is that it is robust to certain types of noise, which may become an issue in integrated circuit (IC) technology with feature sizes in the order of tens of nanometers due to their low noise margin, the effect of high-energy cosmic rays and the low supply voltage. In our framework, the flipping of random individual bits would not affect the system performance because information is encoded in a bit stream. PMID:27047326

  17. The Enteropathy of Prostaglandin Deficiency

    PubMed Central

    Adler, David H.; Phillips, John A.; Cogan, Joy D.; Iverson, Tina M.; Stein, Jeffrey A.; Brenner, David A.; Morrow, Jason D.; Boutaud, Olivier; Oates, John A.

    2009-01-01

    Purpose Small intestinal ulcers are frequent complications of therapy with non-steroidal anti-inflammatory drugs (NSAIDs). We present here a genetic deficiency of eicosanoid biosynthesis that illuminates the mechanism of NSAID-induced ulcers of the small intestine. Methods Eicosanoids and metabolites were measured by isotope-dilution with mass spectrometry. cDNA was obtained by reverse transcription and sequenced following amplification with RT-PCR. Results We investigated the cause of chronic recurrent small intestinal ulcers, small bowel perforations, and gastrointestinal blood loss in a 45 year old male who was not taking any cyclooxygenase inhibitor. Prostaglandin metabolites in urine were significantly depressed. Serum thromboxane B2 (TxB2) production was 4.6% of normal controls (p<0.006) and serum 12-HETE was 1.3% of controls (p<0.005). Optical platelet aggregation with simultaneous monitoring of ATP release demonstrated absent granule secretion in response to ADP and a blunted aggregation response to ADP and collagen, but normal response to arachidonic acid (AA). LTB4 biosynthesis by ionophore activated leukocytes was only 3% of controls and urinary LTE4 was undetectable. These findings suggested deficient AA release from membrane phospholipids by cytosolic phospholipase A2-α (cPLA2-α) which regulates cyclooxygenase and lipoxygenase mediated eicosanoid production by catalyzing the release of their substrate, AA. Sequencing of cPLA2-α cDNA demonstrated 2 heterozygous non-synonymous single base pair mutations: Ser111Pro (S111P) and Arg485His (R485H), as well as a known SNP: Lys651Arg (K651R). Conclusion Characterization of this cPLA2-α deficiency provides support for the importance of prostaglandins in protecting small intestinal integrity, and indicates that loss of prostaglandin biosynthesis is sufficient to produce small intestinal ulcers. PMID:19148786

  18. The changing epidemiology of iodine deficiency.

    PubMed

    Li, Mu; Eastman, Creswell J

    2012-07-01

    Globally, about 2 thousand million people are affected by iodine deficiency. Although endemic goitre is the most visible sign of iodine deficiency, its most devastating consequence is brain damage causing mental retardation in children. The relationship between iodine deficiency and brain damage was not clearly established until the 1980s when the term iodine deficiency disorders (IDDs), which encompass a spectrum of conditions caused by iodine deficiency, was introduced. This paradigm shift in the understanding of the clinical consequences of iodine deficiency led to a change in iodine deficiency assessment. The median urinary iodine excretion level has been recommended as the preferred indicator for monitoring population iodine deficiency status since 2001. The 2007 WHO urinary iodine data in schoolchildren from 130 countries revealed that iodine intake is still insufficient in 47 countries. Furthermore, about one-third of countries lack national estimates of the prevalence of iodine deficiency. The picture that has emerged from available data worldwide over the past two decades is that IDDs are not confined to remote, mountainous areas in developing countries, but are a global public health problem that affects most countries, including developed countries and island nations. The recognition of the universality of iodine deficiency highlights the need to develop and apply new strategies to establish and maintain sustainable IDD elimination and strengthen regular monitoring programmes. PMID:22473332

  19. [LCAT deficiency: a nephrological diagnosis].

    PubMed

    Boscutti, Giuliano; Calabresi, Laura; Pizzolitto, Stefano; Boer, Emanuela; Bosco, Manuela; Mattei, Piero Luigi; Martone, Massimiliano; Milutinovic, Neva; Berbecar, Dorina; Beltram, Elisabetta; Franceschini, Guido

    2011-01-01

    A genetic mendelian autosomal recessive condition of deficiency of lecithin- cholesterol acyltransferase (LCAT) can produce two different diseases: one highly interesting nephrologic picture of complete enzymatic deficiency (lecithin:cholesterol acyltransferase deficiency; OMIM ID #245900; FLD), characterized by the association of dyslipidemia, corneal opacities, anemia and progressive nephropathy; and a partial form (fish eye disease; OMIM ID #136120; FED) with dyslipidemia and progressive corneal opacities only. The diagnosis of FLD falls first of all under the competence of nephrologists, because end-stage renal disease appears to be its most severe outcome. The diagnostic suspicion is based on clinical signs (corneal opacities, more severe anemia than expected for the degree of chronic renal failure, progressive proteinuric nephropathy) combined with histology obtained by kidney biopsy (glomerulopathy evolving toward sclerosis with distinctive lipid deposition). However, the final diagnosis, starting with a finding of extremely low levels of HDL-cholesterol, requires collaboration with lipidology Centers that can perform sophisticated investigations unavailable in common laboratories. To be heterozygous for a mutation of the LCAT gene is one of the monogenic conditions underlying primary hypoalphalipoproteinemia (OMIM ID #604091). This disease, which is characterized by levels of HDL-cholesterol below the 5th percentile of those of the examined population (<28 mg/dL for Italians), has heritability estimates between 40% and 60% and is considered to be a predisposing condition for coronary artery disease. Nevertheless, some monogenic forms, and especially those associated with LCAT deficiency, seem to break the rule, confirming once more the value of a proper diagnosis before drawing prognostic conclusions from a laboratory marker. As in many other rare illnesses, trying to discover all the existing cases will contribute to allow studies broad enough to pave the

  20. Bayesian Inference in Satellite Gravity Inversion

    NASA Technical Reports Server (NTRS)

    Kis, K. I.; Taylor, Patrick T.; Wittmann, G.; Kim, Hyung Rae; Torony, B.; Mayer-Guerr, T.

    2005-01-01

    To solve a geophysical inverse problem means applying measurements to determine the parameters of the selected model. The inverse problem is formulated as the Bayesian inference. The Gaussian probability density functions are applied in the Bayes's equation. The CHAMP satellite gravity data are determined at the altitude of 400 kilometer altitude over the South part of the Pannonian basin. The model of interpretation is the right vertical cylinder. The parameters of the model are obtained from the minimum problem solved by the Simplex method.

  1. Predictive Inference Using Latent Variables with Covariates*

    PubMed Central

    Schofield, Lynne Steuerle; Junker, Brian; Taylor, Lowell J.; Black, Dan A.

    2014-01-01

    Plausible Values (PVs) are a standard multiple imputation tool for analysis of large education survey data that measures latent proficiency variables. When latent proficiency is the dependent variable, we reconsider the standard institutionally-generated PV methodology and find it applies with greater generality than shown previously. When latent proficiency is an independent variable, we show that the standard institutional PV methodology produces biased inference because the institutional conditioning model places restrictions on the form of the secondary analysts’ model. We offer an alternative approach that avoids these biases based on the mixed effects structural equations (MESE) model of Schofield (2008). PMID:25231627

  2. Data free inference with processed data products

    DOE PAGESBeta

    Chowdhary, K.; Najm, H. N.

    2014-07-12

    Here, we consider the context of probabilistic inference of model parameters given error bars or confidence intervals on model output values, when the data is unavailable. We introduce a class of algorithms in a Bayesian framework, relying on maximum entropy arguments and approximate Bayesian computation methods, to generate consistent data with the given summary statistics. Once we obtain consistent data sets, we pool the respective posteriors, to arrive at a single, averaged density on the parameters. This approach allows us to perform accurate forward uncertainty propagation consistent with the reported statistics.

  3. Solar structure: Models and inferences from helioseismology

    SciTech Connect

    Guzik, J.A.

    1998-12-31

    In this review the author summarizes results published during approximately the least three years concerning the state of one-dimensional solar interior modeling. She discusses the effects of refinements to the input physics, motivated by improving the agreement between calculated and observed solar oscillation frequencies, or between calculated and inferred solar structure. She has omitted two- and three-dimensional aspects of the solar structure, such as the rotation profile, detailed modeling of turbulent convection, and magnetic fields, although further progress in refining solar interior models may require including such two- and three-dimensional dynamical effects.

  4. Using alien coins to test whether simple inference is Bayesian.

    PubMed

    Cassey, Peter; Hawkins, Guy E; Donkin, Chris; Brown, Scott D

    2016-03-01

    Reasoning and inference are well-studied aspects of basic cognition that have been explained as statistically optimal Bayesian inference. Using a simplified experimental design, we conducted quantitative comparisons between Bayesian inference and human inference at the level of individuals. In 3 experiments, with more than 13,000 participants, we asked people for prior and posterior inferences about the probability that 1 of 2 coins would generate certain outcomes. Most participants' inferences were inconsistent with Bayes' rule. Only in the simplest version of the task did the majority of participants adhere to Bayes' rule, but even in that case, there was a significant proportion that failed to do so. The current results highlight the importance of close quantitative comparisons between Bayesian inference and human data at the individual-subject level when evaluating models of cognition. (PsycINFO Database Record PMID:26461034

  5. The impact of maternal iron deficiency and iron deficiency anemia on child’s health

    PubMed Central

    Abu-Ouf, Noran M.; Jan, Mohammed M.

    2015-01-01

    Iron deficiency anemia is extremely common, particularly in the developing world, reaching a state of global epidemic. Iron deficiency during pregnancy is one of the leading causes of anemia in infants and young children. Many women go through the entire pregnancy without attaining the minimum required intake of iron. This review aims to determine the impact of maternal iron deficiency and iron deficiency anemia on infants and young children. Extensive literature review revealed that iron deficiency is a global nutritional problem affecting up to 52% of pregnant women. Many of these women are symptomatic. Lack of proper weight gain during pregnancy is an important predictor of iron deficiency. PMID:25719576

  6. Mevalonate kinase deficiency: current perspectives

    PubMed Central

    Favier, Leslie A; Schulert, Grant S

    2016-01-01

    Mevalonate kinase deficiency (MKD) is a recessively inherited autoinflammatory disorder with a spectrum of manifestations, including the well-defined clinical phenotypes of hyperimmunoglobulinemia D and periodic fever syndrome and mevalonic aciduria. Patients with MKD have recurrent attacks of hyperinflammation associated with fever, abdominal pain, arthralgias, and mucocutaneous lesions, and more severely affected patients also have dysmorphisms and central nervous system anomalies. MKD is caused by mutations in the gene encoding mevalonate kinase, with the degree of residual enzyme activity largely determining disease severity. Mevalonate kinase is essential for the biosynthesis of nonsterol isoprenoids, which mediate protein prenylation. Although the precise pathogenesis of MKD remains unclear, increasing evidence suggests that deficiency in protein prenylation leads to innate immune activation and systemic hyperinflammation. Given the emerging understanding of MKD as an autoinflammatory disorder, recent treatment approaches have largely focused on cytokine-directed biologic therapy. Herein, we review the current genetic and pathologic understanding of MKD, its various clinical phenotypes, and the evolving treatment approach for this multifaceted disorder. PMID:27499643

  7. Zinc deficiency in anorexia nervosa.

    PubMed

    Katz, R L; Keen, C L; Litt, I F; Hurley, L S; Kellams-Harrison, K M; Glader, L J

    1987-09-01

    Adolescents with anorexia nervosa were evaluated for clinical and biochemical evidence of zinc deficiency. To assess whether these patients would benefit from zinc supplementation, a double-blind, randomized, controlled trial was conducted. The mean zinc intake of the anorexic group calculated on the basis of three-day dietary records was 7.7 +/- 5.2 mg/day, which is significantly below the recommended daily allowance of 15 mg for adolescents (p less than 0.001). The mean urinary zinc excretion in the anorexic group was 257.1 +/- 212.7 micrograms/24 hours compared to 749.9 +/- 897.8 micrograms/24 hours in the control group (p less than 0.005). This result suggests that the zinc status of anorexia nervosa patients may be compromised due to an inadequate zinc intake. Zinc supplementation (50 mg elemental zinc/day) was followed by a decrease in the level of depression and anxiety as assessed by the Zung Depression Scale (p less than 0.05) and the State-Trait Anxiety Inventory (p less than 0.05), respectively. Our data suggest that individuals with anorexia nervosa may be at risk for zinc deficiency and may respond favorably after zinc supplementation. PMID:3312133

  8. Receptive Field Inference with Localized Priors

    PubMed Central

    Park, Mijung; Pillow, Jonathan W.

    2011-01-01

    The linear receptive field describes a mapping from sensory stimuli to a one-dimensional variable governing a neuron's spike response. However, traditional receptive field estimators such as the spike-triggered average converge slowly and often require large amounts of data. Bayesian methods seek to overcome this problem by biasing estimates towards solutions that are more likely a priori, typically those with small, smooth, or sparse coefficients. Here we introduce a novel Bayesian receptive field estimator designed to incorporate locality, a powerful form of prior information about receptive field structure. The key to our approach is a hierarchical receptive field model that flexibly adapts to localized structure in both spacetime and spatiotemporal frequency, using an inference method known as empirical Bayes. We refer to our method as automatic locality determination (ALD), and show that it can accurately recover various types of smooth, sparse, and localized receptive fields. We apply ALD to neural data from retinal ganglion cells and V1 simple cells, and find it achieves error rates several times lower than standard estimators. Thus, estimates of comparable accuracy can be achieved with substantially less data. Finally, we introduce a computationally efficient Markov Chain Monte Carlo (MCMC) algorithm for fully Bayesian inference under the ALD prior, yielding accurate Bayesian confidence intervals for small or noisy datasets. PMID:22046110

  9. Causal Inference for Spatial Constancy across Saccades.

    PubMed

    Atsma, Jeroen; Maij, Femke; Koppen, Mathieu; Irwin, David E; Medendorp, W Pieter

    2016-03-01

    Our ability to interact with the environment hinges on creating a stable visual world despite the continuous changes in retinal input. To achieve visual stability, the brain must distinguish the retinal image shifts caused by eye movements and shifts due to movements of the visual scene. This process appears not to be flawless: during saccades, we often fail to detect whether visual objects remain stable or move, which is called saccadic suppression of displacement (SSD). How does the brain evaluate the memorized information of the presaccadic scene and the actual visual feedback of the postsaccadic visual scene in the computations for visual stability? Using a SSD task, we test how participants localize the presaccadic position of the fixation target, the saccade target or a peripheral non-foveated target that was displaced parallel or orthogonal during a horizontal saccade, and subsequently viewed for three different durations. Results showed different localization errors of the three targets, depending on the viewing time of the postsaccadic stimulus and its spatial separation from the presaccadic location. We modeled the data through a Bayesian causal inference mechanism, in which at the trial level an optimal mixing of two possible strategies, integration vs. separation of the presaccadic memory and the postsaccadic sensory signals, is applied. Fits of this model generally outperformed other plausible decision strategies for producing SSD. Our findings suggest that humans exploit a Bayesian inference process with two causal structures to mediate visual stability. PMID:26967730

  10. Phylogenetic Inference From Conserved sites Alignments

    SciTech Connect

    grundy, W.N.; Naylor, G.J.P.

    1999-08-15

    Molecular sequences provide a rich source of data for inferring the phylogenetic relationships among species. However, recent work indicates that even an accurate multiple alignment of a large sequence set may yield an incorrect phylogeny and that the quality of the phylogenetic tree improves when the input consists only of the highly conserved, motif regions of the alignment. This work introduces two methods of producing multiple alignments that include only the conserved regions of the initial alignment. The first method retains conserved motifs, whereas the second retains individual conserved sites in the initial alignment. Using parsimony analysis on a mitochondrial data set containing 19 species among which the phylogenetic relationships are widely accepted, both conserved alignment methods produce better phylogenetic trees than the complete alignment. Unlike any of the 19 inference methods used before to analyze this data, both methods produce trees that are completely consistent with the known phylogeny. The motif-based method employs far fewer alignment sites for comparable error rates. For a larger data set containing mitochondrial sequences from 39 species, the site-based method produces a phylogenetic tree that is largely consistent with known phylogenetic relationships and suggests several novel placements.

  11. Inferring differentiation pathways from gene expression

    PubMed Central

    Costa, Ivan G.; Roepcke, Stefan; Hafemeister, Christoph; Schliep, Alexander

    2008-01-01

    Motivation: The regulation of proliferation and differentiation of embryonic and adult stem cells into mature cells is central to developmental biology. Gene expression measured in distinguishable developmental stages helps to elucidate underlying molecular processes. In previous work we showed that functional gene modules, which act distinctly in the course of development, can be represented by a mixture of trees. In general, the similarities in the gene expression programs of cell populations reflect the similarities in the differentiation path. Results: We propose a novel model for gene expression profiles and an unsupervised learning method to estimate developmental similarity and infer differentiation pathways. We assess the performance of our model on simulated data and compare it with favorable results to related methods. We also infer differentiation pathways and predict functional modules in gene expression data of lymphoid development. Conclusions: We demonstrate for the first time how, in principal, the incorporation of structural knowledge about the dependence structure helps to reveal differentiation pathways and potentially relevant functional gene modules from microarray datasets. Our method applies in any area of developmental biology where it is possible to obtain cells of distinguishable differentiation stages. Availability: The implementation of our method (GPL license), data and additional results are available at http://algorithmics.molgen.mpg.de/Supplements/InfDif/ Contact: filho@molgen.mpg.de, schliep@molgen.mpg.de Supplementary information: Supplementary data is available at Bioinformatics online. PMID:18586709

  12. Natural frequencies facilitate diagnostic inferences of managers.

    PubMed

    Hoffrage, Ulrich; Hafenbrädl, Sebastian; Bouquet, Cyril

    2015-01-01

    In Bayesian inference tasks, information about base rates as well as hit rate and false-alarm rate needs to be integrated according to Bayes' rule after the result of a diagnostic test became known. Numerous studies have found that presenting information in a Bayesian inference task in terms of natural frequencies leads to better performance compared to variants with information presented in terms of probabilities or percentages. Natural frequencies are the tallies in a natural sample in which hit rate and false-alarm rate are not normalized with respect to base rates. The present research replicates the beneficial effect of natural frequencies with four tasks from the domain of management, and with management students as well as experienced executives as participants. The percentage of Bayesian responses was almost twice as high when information was presented in natural frequencies compared to a presentation in terms of percentages. In contrast to most tasks previously studied, the majority of numerical responses were lower than the Bayesian solutions. Having heard of Bayes' rule prior to the study did not affect Bayesian performance. An implication of our work is that textbooks explaining Bayes' rule should teach how to represent information in terms of natural frequencies instead of how to plug probabilities or percentages into a formula. PMID:26157397

  13. Inferring epigenetic dynamics from kin correlations.

    PubMed

    Hormoz, Sahand; Desprat, Nicolas; Shraiman, Boris I

    2015-05-01

    Populations of isogenic embryonic stem cells or clonal bacteria often exhibit extensive phenotypic heterogeneity that arises from intrinsic stochastic dynamics of cells. The phenotypic state of a cell can be transmitted epigenetically in cell division, leading to correlations in the states of cells related by descent. The extent of these correlations is determined by the rates of transitions between the phenotypic states. Therefore, a snapshot of the phenotypes of a collection of cells with known genealogical structure contains information on phenotypic dynamics. Here, we use a model of phenotypic dynamics on a genealogical tree to define an inference method that allows extraction of an approximate probabilistic description of the dynamics from observed phenotype correlations as a function of the degree of kinship. The approach is tested and validated on the example of Pyoverdine dynamics in Pseudomonas aeruginosa colonies. Interestingly, we find that correlations among pairs and triples of distant relatives have a simple but nontrivial structure indicating that observed phenotypic dynamics on the genealogical tree is approximately conformal--a symmetry characteristic of critical behavior in physical systems. The proposed inference method is sufficiently general to be applied in any system where lineage information is available. PMID:25902540

  14. Inferring social ties from geographic coincidences

    PubMed Central

    Crandall, David J.; Backstrom, Lars; Cosley, Dan; Suri, Siddharth; Huttenlocher, Daniel; Kleinberg, Jon

    2010-01-01

    We investigate the extent to which social ties between people can be inferred from co-occurrence in time and space: Given that two people have been in approximately the same geographic locale at approximately the same time, on multiple occasions, how likely are they to know each other? Furthermore, how does this likelihood depend on the spatial and temporal proximity of the co-occurrences? Such issues arise in data originating in both online and offline domains as well as settings that capture interfaces between online and offline behavior. Here we develop a framework for quantifying the answers to such questions, and we apply this framework to publicly available data from a social media site, finding that even a very small number of co-occurrences can result in a high empirical likelihood of a social tie. We then present probabilistic models showing how such large probabilities can arise from a natural model of proximity and co-occurrence in the presence of social ties. In addition to providing a method for establishing some of the first quantifiable estimates of these measures, our findings have potential privacy implications, particularly for the ways in which social structures can be inferred from public online records that capture individuals’ physical locations over time. PMID:21148099

  15. Inferring Seizure Frequency From Brief EEG Recordings

    PubMed Central

    Westover, M. Brandon; Bianchi, Matt T.; Shafi, Mouhsin; Hoch, Daniel B.; Cole, Andrew J.; Chiappa, Keith; Cash, Sydney S.

    2012-01-01

    Routine EEGs remain a cornerstone test in caring for people with epilepsy. Although rare, a self-limited seizure (clinical or electrographic only) may be observed during such brief EEGs. The implications of observing a seizure in this situation, especially with respect to inferring the underlying seizure frequency, are unclear. The issue is complicated by the inaccuracy of patient-reported estimations of seizure frequency. The treating clinician is often left to wonder whether the single seizure indicates very frequent seizures, or if it is of lesser significance. We applied standard concepts of probabilistic inference to a simple model of seizure incidence to provide some guidance for clinicians facing this situation. Our analysis establishes upper and lower bounds on the seizure rate implied by observing a single seizure during routine EEG. Not surprisingly, with additional information regarding the expected seizure rate, these bounds can be further constrained. This framework should aid the clinician in applying a more principled approach toward decision making in the setting of a single seizure on a routine EEG. PMID:23545768

  16. Active inference, eye movements and oculomotor delays.

    PubMed

    Perrinet, Laurent U; Adams, Rick A; Friston, Karl J

    2014-12-01

    This paper considers the problem of sensorimotor delays in the optimal control of (smooth) eye movements under uncertainty. Specifically, we consider delays in the visuo-oculomotor loop and their implications for active inference. Active inference uses a generalisation of Kalman filtering to provide Bayes optimal estimates of hidden states and action in generalised coordinates of motion. Representing hidden states in generalised coordinates provides a simple way of compensating for both sensory and oculomotor delays. The efficacy of this scheme is illustrated using neuronal simulations of pursuit initiation responses, with and without compensation. We then consider an extension of the generative model to simulate smooth pursuit eye movements-in which the visuo-oculomotor system believes both the target and its centre of gaze are attracted to a (hidden) point moving in the visual field. Finally, the generative model is equipped with a hierarchical structure, so that it can recognise and remember unseen (occluded) trajectories and emit anticipatory responses. These simulations speak to a straightforward and neurobiologically plausible solution to the generic problem of integrating information from different sources with different temporal delays and the particular difficulties encountered when a system-like the oculomotor system-tries to control its environment with delayed signals. PMID:25128318

  17. Toddlers infer unobserved causes for spontaneous events

    PubMed Central

    Muentener, Paul; Schulz, Laura

    2014-01-01

    Previous research suggests that children infer the presence of unobserved causes when objects appear to move spontaneously. Are such inferences limited to motion events or do children assume that unexplained physical events have causes more generally? Here we introduce an apparently spontaneous event and ask whether, even in the absence of spatiotemporal and co-variation cues linking the events, toddlers treat a plausible variable as a cause of the event. Toddlers (24 months) saw a toy that appeared to light up either spontaneously or after an experimenter’s action. Toddlers were also introduced to a button but were not shown any predictive relation between the button and the light. Across three different dependent measures of exploration, predictive looking (Study 1), prompted intervention (Study 2), and spontaneous exploration (Study 3), toddlers were more likely to represent the button as a cause of the light when the event appeared to occur spontaneously. In Study 4, we found that even in the absence of a plausible candidate cause, toddlers engaged in selective exploration when the light appeared to activate spontaneously. These results suggest that toddlers’ exploration is guided by the causal explanatory power of events. PMID:25566161

  18. Spatial Inference for Distributed Remote Sensing Data

    NASA Astrophysics Data System (ADS)

    Braverman, A. J.; Katzfuss, M.; Nguyen, H.

    2014-12-01

    Remote sensing data are inherently spatial, and a substantial portion of their value for scientific analyses derives from the information they can provide about spatially dependent processes. Geophysical variables such as atmopsheric temperature, cloud properties, humidity, aerosols and carbon dioxide all exhibit spatial patterns, and satellite observations can help us learn about the physical mechanisms driving them. However, remote sensing observations are often noisy and incomplete, so inferring properties of true geophysical fields from them requires some care. These data can also be massive, which is both a blessing and a curse: using more data drives uncertainties down, but also drives costs up, particularly when data are stored on different computers or in different physical locations. In this talk I will discuss a methodology for spatial inference on massive, distributed data sets that does not require moving large volumes of data. The idea is based on a combination of ideas including modeling spatial covariance structures with low-rank covariance matrices, and distributed estimation in sensor or wireless networks.

  19. An Ada inference engine for expert systems

    NASA Technical Reports Server (NTRS)

    Lavallee, David B.

    1986-01-01

    The purpose is to investigate the feasibility of using Ada for rule-based expert systems with real-time performance requirements. This includes exploring the Ada features which give improved performance to expert systems as well as optimizing the tradeoffs or workarounds that the use of Ada may require. A prototype inference engine was built using Ada, and rule firing rates in excess of 500 per second were demonstrated on a single MC68000 processor. The knowledge base uses a directed acyclic graph to represent production lines. The graph allows the use of AND, OR, and NOT logical operators. The inference engine uses a combination of both forward and backward chaining in order to reach goals as quickly as possible. Future efforts will include additional investigation of multiprocessing to improve performance and creating a user interface allowing rule input in an Ada-like syntax. Investigation of multitasking and alternate knowledge base representations will help to analyze some of the performance issues as they relate to larger problems.

  20. Causal Inference for Spatial Constancy across Saccades

    PubMed Central

    Atsma, Jeroen; Maij, Femke; Koppen, Mathieu; Irwin, David E.; Medendorp, W. Pieter

    2016-01-01

    Our ability to interact with the environment hinges on creating a stable visual world despite the continuous changes in retinal input. To achieve visual stability, the brain must distinguish the retinal image shifts caused by eye movements and shifts due to movements of the visual scene. This process appears not to be flawless: during saccades, we often fail to detect whether visual objects remain stable or move, which is called saccadic suppression of displacement (SSD). How does the brain evaluate the memorized information of the presaccadic scene and the actual visual feedback of the postsaccadic visual scene in the computations for visual stability? Using a SSD task, we test how participants localize the presaccadic position of the fixation target, the saccade target or a peripheral non-foveated target that was displaced parallel or orthogonal during a horizontal saccade, and subsequently viewed for three different durations. Results showed different localization errors of the three targets, depending on the viewing time of the postsaccadic stimulus and its spatial separation from the presaccadic location. We modeled the data through a Bayesian causal inference mechanism, in which at the trial level an optimal mixing of two possible strategies, integration vs. separation of the presaccadic memory and the postsaccadic sensory signals, is applied. Fits of this model generally outperformed other plausible decision strategies for producing SSD. Our findings suggest that humans exploit a Bayesian inference process with two causal structures to mediate visual stability. PMID:26967730

  1. Information Theory, Inference and Learning Algorithms

    NASA Astrophysics Data System (ADS)

    Mackay, David J. C.

    2003-10-01

    Information theory and inference, often taught separately, are here united in one entertaining textbook. These topics lie at the heart of many exciting areas of contemporary science and engineering - communication, signal processing, data mining, machine learning, pattern recognition, computational neuroscience, bioinformatics, and cryptography. This textbook introduces theory in tandem with applications. Information theory is taught alongside practical communication systems, such as arithmetic coding for data compression and sparse-graph codes for error-correction. A toolbox of inference techniques, including message-passing algorithms, Monte Carlo methods, and variational approximations, are developed alongside applications of these tools to clustering, convolutional codes, independent component analysis, and neural networks. The final part of the book describes the state of the art in error-correcting codes, including low-density parity-check codes, turbo codes, and digital fountain codes -- the twenty-first century standards for satellite communications, disk drives, and data broadcast. Richly illustrated, filled with worked examples and over 400 exercises, some with detailed solutions, David MacKay's groundbreaking book is ideal for self-learning and for undergraduate or graduate courses. Interludes on crosswords, evolution, and sex provide entertainment along the way. In sum, this is a textbook on information, communication, and coding for a new generation of students, and an unparalleled entry point into these subjects for professionals in areas as diverse as computational biology, financial engineering, and machine learning.

  2. Natural frequencies facilitate diagnostic inferences of managers

    PubMed Central

    Hoffrage, Ulrich; Hafenbrädl, Sebastian; Bouquet, Cyril

    2015-01-01

    In Bayesian inference tasks, information about base rates as well as hit rate and false-alarm rate needs to be integrated according to Bayes’ rule after the result of a diagnostic test became known. Numerous studies have found that presenting information in a Bayesian inference task in terms of natural frequencies leads to better performance compared to variants with information presented in terms of probabilities or percentages. Natural frequencies are the tallies in a natural sample in which hit rate and false-alarm rate are not normalized with respect to base rates. The present research replicates the beneficial effect of natural frequencies with four tasks from the domain of management, and with management students as well as experienced executives as participants. The percentage of Bayesian responses was almost twice as high when information was presented in natural frequencies compared to a presentation in terms of percentages. In contrast to most tasks previously studied, the majority of numerical responses were lower than the Bayesian solutions. Having heard of Bayes’ rule prior to the study did not affect Bayesian performance. An implication of our work is that textbooks explaining Bayes’ rule should teach how to represent information in terms of natural frequencies instead of how to plug probabilities or percentages into a formula. PMID:26157397

  3. Inferring Neuronal Dynamics from Calcium Imaging Data Using Biophysical Models and Bayesian Inference

    PubMed Central

    Rahmati, Vahid; Kirmse, Knut; Marković, Dimitrije; Holthoff, Knut; Kiebel, Stefan J.

    2016-01-01

    Calcium imaging has been used as a promising technique to monitor the dynamic activity of neuronal populations. However, the calcium trace is temporally smeared which restricts the extraction of quantities of interest such as spike trains of individual neurons. To address this issue, spike reconstruction algorithms have been introduced. One limitation of such reconstructions is that the underlying models are not informed about the biophysics of spike and burst generations. Such existing prior knowledge might be useful for constraining the possible solutions of spikes. Here we describe, in a novel Bayesian approach, how principled knowledge about neuronal dynamics can be employed to infer biophysical variables and parameters from fluorescence traces. By using both synthetic and in vitro recorded fluorescence traces, we demonstrate that the new approach is able to reconstruct different repetitive spiking and/or bursting patterns with accurate single spike resolution. Furthermore, we show that the high inference precision of the new approach is preserved even if the fluorescence trace is rather noisy or if the fluorescence transients show slow rise kinetics lasting several hundred milliseconds, and inhomogeneous rise and decay times. In addition, we discuss the use of the new approach for inferring parameter changes, e.g. due to a pharmacological intervention, as well as for inferring complex characteristics of immature neuronal circuits. PMID:26894748

  4. Congenital longitudinal deficiency of the tibia.

    PubMed

    Spiegel, D A; Loder, R T; Crandall, R C

    2003-01-01

    We performed a clinical and radiographic review of 15 patients (19 limbs) with longitudinal deficiency of the tibia treated between 1981 and 2001. Ten limbs with Kalamchi type I deficiencies were managed by through-knee amputation. Five type II deficiencies were treated by foot ablation and tibiofibular synostosis, either at the same time or staged, but prosthetic problems may arise from varus alignment and prominence of the proximal fibula. Patients with type III deficiencies (four cases) were treated by foot ablation. Prosthetic problems relating to proximal or distal tibiofibular instability may necessitate additional surgical intervention. PMID:12879290

  5. Children's inference generation: The role of vocabulary and working memory.

    PubMed

    Currie, Nicola Kate; Cain, Kate

    2015-09-01

    Inferences are crucial to successful discourse comprehension. We assessed the contributions of vocabulary and working memory to inference making in children aged 5 and 6years (n=44), 7 and 8years (n=43), and 9 and 10years (n=43). Children listened to short narratives and answered questions to assess local and global coherence inferences after each one. Analysis of variance (ANOVA) confirmed developmental improvements on both types of inference. Although standardized measures of both vocabulary and working memory were correlated with inference making, multiple regression analyses determined that vocabulary was the key predictor. For local coherence inferences, only vocabulary predicted unique variance for the 6- and 8-year-olds; in contrast, none of the variables predicted performance for the 10-year-olds. For global coherence inferences, vocabulary was the only unique predictor for each age group. Mediation analysis confirmed that although working memory was associated with the ability to generate local and global coherence inferences in 6- to 10-year-olds, the effect was mediated by vocabulary. We conclude that vocabulary knowledge supports inference making in two ways: through knowledge of word meanings required to generate inferences and through its contribution to memory processes. PMID:25930678

  6. Inferring the temperature dependence of population parameters: the effects of experimental design and inference algorithm.

    PubMed

    Palamara, Gian Marco; Childs, Dylan Z; Clements, Christopher F; Petchey, Owen L; Plebani, Marco; Smith, Matthew J

    2014-12-01

    Understanding and quantifying the temperature dependence of population parameters, such as intrinsic growth rate and carrying capacity, is critical for predicting the ecological responses to environmental change. Many studies provide empirical estimates of such temperature dependencies, but a thorough investigation of the methods used to infer them has not been performed yet. We created artificial population time series using a stochastic logistic model parameterized with the Arrhenius equation, so that activation energy drives the temperature dependence of population parameters. We simulated different experimental designs and used different inference methods, varying the likelihood functions and other aspects of the parameter estimation methods. Finally, we applied the best performing inference methods to real data for the species Paramecium caudatum. The relative error of the estimates of activation energy varied between 5% and 30%. The fraction of habitat sampled played the most important role in determining the relative error; sampling at least 1% of the habitat kept it below 50%. We found that methods that simultaneously use all time series data (direct methods) and methods that estimate population parameters separately for each temperature (indirect methods) are complementary. Indirect methods provide a clearer insight into the shape of the functional form describing the temperature dependence of population parameters; direct methods enable a more accurate estimation of the parameters of such functional forms. Using both methods, we found that growth rate and carrying capacity of Paramecium caudatum scale with temperature according to different activation energies. Our study shows how careful choice of experimental design and inference methods can increase the accuracy of the inferred relationships between temperature and population parameters. The comparison of estimation methods provided here can increase the accuracy of model predictions, with important

  7. Inferences of weekly cycles in summertime rainfall

    NASA Astrophysics Data System (ADS)

    Tuttle, John D.; Carbone, Richard E.

    2011-10-01

    In several continental regions a weekly cycle of air pollution aerosols has been observed. It is usually characterized by concentration minima on weekends (Saturday and Sunday) and maxima on weekdays (Tuesday-Friday). Several studies have associated varying aerosol concentrations with precipitation production and attempted to determine whether or not there is a corresponding weekly cycle of precipitation. Results to date have been mixed. Here we examine a 12 year national composited radar data set for evidence of weekly precipitation cycles during the warm season (June-August). Various statistical quantities are calculated and subjected to "bootstrap" testing in order to assess significance. In many parts of the United States, warm season precipitation is relatively infrequent, with a few extreme events contributing to a large percentage of the total 12 year rainfall. For this reason, the statistics are often difficult to interpret. The general area east of the Mississippi River and north of 37°N contains regions where 25%-50% daily rainfall increases are inferred for weekdays (Tuesday-Friday) relative to weekends. The statistics suggest that western Pennsylvania is the largest and most likely contiguous region to have a weekly cycle. Parts of northern Florida and southeastern coastal areas infer a reverse-phase cycle, with less rainfall during the week than on weekends. Spot checks of surface rain gauge data confirm the phase of these radar-observed anomalies in both Pennsylvania and Florida. While there are indications of a weekly cycle in other locations of the United States, the degree of confidence is considerably lower. There is a strong statistical inference of weekday rainfall maxima over a net 8% of the area examined, which is approximately twice the area of cities. Future examination of lofted aerosol content, related condensation/ice nuclei spectra, and knowledge of the convective dynamical regime are needed in order to assess how anthropogenic aerosols

  8. Primary Carnitine Deficiency and Cardiomyopathy

    PubMed Central

    Fu, Lijun; Huang, Meirong

    2013-01-01

    Carnitine is essential for the transfer of long-chain fatty acids from the cytosol into mitochondria for subsequent β-oxidation. A lack of carnitine results in impaired energy production from long-chain fatty acids, especially during periods of fasting or stress. Primary carnitine deficiency (PCD) is an autosomal recessive disorder of mitochondrial β-oxidation resulting from defective carnitine transport and is one of the rare treatable etiologies of metabolic cardiomyopathies. Patients affected with the disease may present with acute metabolic decompensation during infancy or with severe cardiomyopathy in childhood. Early recognition of the disease and treatment with L-carnitine may be life-saving. In this review article, the pathophysiology, clinical presentation, diagnosis, treatment and prognosis of PCD are discussed, with a focus on cardiac involvements. PMID:24385988

  9. Photodissociation of neutron deficient nuclei

    NASA Astrophysics Data System (ADS)

    Sonnabend, K.; Babilon, M.; Hasper, J.; Müller, S.; Zarza, M.; Zilges, A.

    2006-03-01

    The knowledge of the cross sections for photodissociation reactions like e.g. (γ, n) of neutron deficient nuclei is of crucial interest for network calculations predicting the abundances of the so-called p nuclei. However, only single cross sections have been measured up to now, i.e., one has to rely nearly fully on theoretical predictions. While the cross sections of stable isotopes are accessible by experiments using real photons, the bulk of the involved reactions starts from unstable nuclei. Coulomb dissociation (CD) experiments in inverse kinematics might be a key to expand the experimental database for p-process network calculations. The approach to test the accuracy of the CD method is explained.

  10. [Iron deficiency in the elderly].

    PubMed

    Helsen, Tuur; Joosten, Etienne

    2016-06-01

    Anemia is a common diagnosis in the geriatric population, especially in institutionalized and hospitalized elderly. Most common etiologies for anemia in elderly people admitted to a geriatric ward are iron-deficiency anemia and anemia associated with chronic disease. Determination of serum ferritin is the most used assay in the differential diagnosis, despite low sensitivity and moderate specificity. New insights into iron homeostasis lead to new diagnostic assays such as serum hepcidin, serum transferrin receptor and reticulocyte hemoglobin equivalent.Importance of proper diagnosis and treatment for this population is large since there is a correlation between anemia and morbidity - mortality. Anemia is usually defined as hemoglobin less than 12 g/dl for women and less than 13 g/dl for men. There is no consensus for which hemoglobinvalue an investigation into underlying pathology is obligatory. This needs to be evaluated depending on functional condition of the patient. PMID:27106490

  11. Perspectives on nutritional iron deficiency.

    PubMed

    Hallberg, L

    2001-01-01

    Nutritional iron deficiency (ID) is caused by an intake of dietary iron insufficient to cover physiological iron requirements. Studies on iron absorption from whole diets have examined relationships between dietary iron bioavailability/absorption, iron losses, and amounts of stored iron. New insights have been obtained into regulation of iron absorption and expected rates of changes of iron stores or hemoglobin iron deficits when bioavailability or iron content of the diet has been modified and when losses of iron occur. Negative effects of ID are probably related to age, up to about 20 years, explaining some of earlier controversies. Difficulties in establishing the prevalence of mild ID are outlined. The degree of underestimation of the prevalence of mild ID when using multiple diagnostic criteria is discussed. It is suggested that current low-energy lifestyles are a common denominator for the current high prevalence not only of ID but also of obesity, diabetes, and osteoporosis. PMID:11375427

  12. SERIES - Satellite Emission Range Inferred Earth Surveying

    NASA Technical Reports Server (NTRS)

    Macdoran, P. F.; Spitzmesser, D. J.; Buennagel, L. A.

    1983-01-01

    The Satellite Emission Range Inferred Earth Surveying (SERIES) concept is based on the utilization of NAVSTAR Global Positioning System (GPS) radio transmissions without any satellite modifications and in a totally passive mode. The SERIES stations are equipped with lightweight 1.5 m diameter dish antennas mounted on trailers. A series baseline measurement accuracy demonstration is considered, taking into account a 100 meter baseline estimation from approximately one hour of differential Doppler data. It is planned to conduct the next phase of experiments on a 150 m baseline. Attention is given to details regarding future baseline measurement accuracy demonstrations, aspects of ionospheric calibration in connection with subdecimeter baseline accuracy requirements of geodesy, and advantages related to the use of the differential Doppler or pseudoranging mode.

  13. Chloroplast Phylogenomic Inference of Green Algae Relationships

    PubMed Central

    Sun, Linhua; Fang, Ling; Zhang, Zhenhua; Chang, Xin; Penny, David; Zhong, Bojian

    2016-01-01

    The green algal phylum Chlorophyta has six diverse classes, but the phylogenetic relationship of the classes within Chlorophyta remains uncertain. In order to better understand the ancient Chlorophyta evolution, we have applied a site pattern sorting method to study compositional heterogeneity and the model fit in the green algal chloroplast genomic data. We show that the fastest-evolving sites are significantly correlated with among-site compositional heterogeneity, and these sites have a much poorer fit to the evolutionary model. Our phylogenomic analyses suggest that the class Chlorophyceae is a monophyletic group, and the classes Ulvophyceae, Trebouxiophyceae and Prasinophyceae are non-monophyletic groups. Our proposed phylogenetic tree of Chlorophyta will offer new insights to investigate ancient green algae evolution, and our analytical framework will provide a useful approach for evaluating and mitigating the potential errors of phylogenomic inferences. PMID:26846729

  14. Migration of objects and inferences across episodes.

    PubMed

    Hannigan, Sharon L; Reinitz, Mark Tippens

    2003-04-01

    Participants viewed episodes in the form of a series of photographs portraying ordinary routines (e.g., eating at a restaurant) and later received a recognition test. In Experiment 1, it was shown that objects (e.g., a vase of flowers, a pewter lantern) that appeared in a single episode during the study phase migrated between memories of episodes described by the same abstract schema (e.g., from Restaurant Episode A at study to Restaurant Episode B at test), and not between episodes anchored by different schemas. In Experiment 2, it was demonstrated that backward causal inferences from one study episode influenced memories of other episodes described by the same schema, and that high-schema-relevant items viewed in one episode were sometimes remembered as having occurred in another episode of the same schematic type. PMID:12795485

  15. cosmoabc: Likelihood-free inference for cosmology

    NASA Astrophysics Data System (ADS)

    Ishida, Emille E. O.; Vitenti, Sandro D. P.; Penna-Lima, Mariana; Trindade, Arlindo M.; Cisewski, Jessi; M.; de Souza, Rafael; Cameron, Ewan; Busti, Vinicius C.

    2015-05-01

    Approximate Bayesian Computation (ABC) enables parameter inference for complex physical systems in cases where the true likelihood function is unknown, unavailable, or computationally too expensive. It relies on the forward simulation of mock data and comparison between observed and synthetic catalogs. cosmoabc is a Python Approximate Bayesian Computation (ABC) sampler featuring a Population Monte Carlo variation of the original ABC algorithm, which uses an adaptive importance sampling scheme. The code can be coupled to an external simulator to allow incorporation of arbitrary distance and prior functions. When coupled with the numcosmo library, it has been used to estimate posterior probability distributions over cosmological parameters based on measurements of galaxy clusters number counts without computing the likelihood function.

  16. ExplainHoudini: Making Houdini Inference Transparent

    NASA Astrophysics Data System (ADS)

    Lahiri, Shuvendu K.; Vanegue, Julien

    Houdini is a simple yet scalable technique for annotation inference for modular contract checking. The input to Houdini is a set of candidate annotations, and the output is a consistent subset of these candidates. Since this technique is most useful as an annotation assistant for user-guided refinement of annotations, understanding the reason for the removal of annotations is crucial for a user to refine the set of annotations, and classify false errors easily. This is especially true for applying Houdini to large legacy modules with thousands of procedures and deep call chains. In this work we present a method ExplainHoudini that explains the reason why a given candidate was removed, purely in terms of the existing candidates. We have implemented this algorithm and provide preliminary experience of applying it on large modules.

  17. Automated adaptive inference of phenomenological dynamical models

    PubMed Central

    Daniels, Bryan C.; Nemenman, Ilya

    2015-01-01

    Dynamics of complex systems is often driven by large and intricate networks of microscopic interactions, whose sheer size obfuscates understanding. With limited experimental data, many parameters of such dynamics are unknown, and thus detailed, mechanistic models risk overfitting and making faulty predictions. At the other extreme, simple ad hoc models often miss defining features of the underlying systems. Here we develop an approach that instead constructs phenomenological, coarse-grained models of network dynamics that automatically adapt their complexity to the available data. Such adaptive models produce accurate predictions even when microscopic details are unknown. The approach is computationally tractable, even for a relatively large number of dynamical variables. Using simulated data, it correctly infers the phase space structure for planetary motion, avoids overfitting in a biological signalling system and produces accurate predictions for yeast glycolysis with tens of data points and over half of the interacting species unobserved. PMID:26293508

  18. Inferring coalescence times from DNA sequence data.

    PubMed

    Tavaré, S; Balding, D J; Griffiths, R C; Donnelly, P

    1997-02-01

    The paper is concerned with methods for the estimation of the coalescence time (time since the most recent common ancestor) of a sample of intraspecies DNA sequences. The methods take advantage of prior knowledge of population demography, in addition to the molecular data. While some theoretical results are presented, a central focus is on computational methods. These methods are easy to implement, and, since explicit formulae tend to be either unavailable or unilluminating, they are also more useful and more informative in most applications. Extensions are presented that allow for the effects of uncertainty in our knowledge of population size and mutation rates, for variability in population sizes, for regions of different mutation rate, and for inference concerning the coalescence time of the entire population. The methods are illustrated using recent data from the human Y chromosome. PMID:9071603

  19. Inferring biological dynamics in heterogeneous cellular environments

    NASA Astrophysics Data System (ADS)

    Pressé, Steve

    In complex environments, it often appears that biomolecules such as proteins do not diffuse normally. That is, their mean square displacement does not scale linearly with time. This anomalous diffusion happens for multiple reasons: proteins can bind to structures and other proteins; fluorophores used to label proteins may flicker or blink making it appear that the labeled protein is diffusing anomalously; and proteins can diffuse in differently crowded environments. Here we describe methods for learning about such processes from imaging data collected inside the heterogeneous environment of the living cell. Refs.: ''Inferring Diffusional Dynamics from FCS in Heterogeneous Nuclear Environments'' Konstantinos Tsekouras, Amanda Siegel, Richard N. Day, Steve Pressé*, Biophys. J. , 109, 7 (2015). ''A data-driven alternative to the fractional Fokker-Planck equation'' Steve Pressé*, J. Stat. Phys.: Th. and Expmt. , P07009 (2015).

  20. Inference of fitness from genealogical trees

    NASA Astrophysics Data System (ADS)

    Vucelja, Marija; Dayarian, Adel; Shraiman, Boris

    2013-03-01

    Natural populations are fitness diverse and can have numerous genes under selection. The genealogical trees, that one obtains by sampling, often bear hallmarks of selection, such multiple mergers, asymmetric tree branches and long terminal branches (the trees are squished towards the root). These are qualitative differences compared to trees in the absence of selection. We propose a theoretical model that links the morphology of a tree with the fitness of the leaves. We obtain multipoint correlation functions of the fitness along the tree. In this way we are able extract some quantitative information about the strength of selection from data-reconstructed trees. The extensions of this approach can potentially be useful for inferring relative fitness of sequenced genomes of tumors and for predicting viral outbreaks.

  1. Cancer Evolution: Mathematical Models and Computational Inference

    PubMed Central

    Beerenwinkel, Niko; Schwarz, Roland F.; Gerstung, Moritz; Markowetz, Florian

    2015-01-01

    Cancer is a somatic evolutionary process characterized by the accumulation of mutations, which contribute to tumor growth, clinical progression, immune escape, and drug resistance development. Evolutionary theory can be used to analyze the dynamics of tumor cell populations and to make inference about the evolutionary history of a tumor from molecular data. We review recent approaches to modeling the evolution of cancer, including population dynamics models of tumor initiation and progression, phylogenetic methods to model the evolutionary relationship between tumor subclones, and probabilistic graphical models to describe dependencies among mutations. Evolutionary modeling helps to understand how tumors arise and will also play an increasingly important prognostic role in predicting disease progression and the outcome of medical interventions, such as targeted therapy. PMID:25293804

  2. Single-Trial Inference on Visual Attention

    NASA Astrophysics Data System (ADS)

    Dyrholm, Mads; Kyllingsbæk, Søren; Vangkilde, Signe; Habekost, Thomas; Bundesen, Claus

    2011-06-01

    In this paper we take a step towards single-trial behavioral modeling within a Theory of Visual Attention (TVA). In selective attention tasks, such as the Partial Report paradigm, the subject is asked to ignore distractors and only report stimuli that belong to the target class. Nothing about a distractor is observed directly in the subject's overt behavior, hence behavioral modeling of such trials involves out-marginalizing the variables that represent the distractors' influence on behavior. In this paper we derive equations for inferring a latent representation of the distractors on a Partial Report trial. This result retrodicts a latent attentional state of the subject using the observed response from that particular trial and thus differs from other predictions made with TVA which are based on expected values of observed variables. We show an example of the result in single-trial analysis of an occipital EEG component.

  3. BINOCh: binding inference from nucleosome occupancy changes

    PubMed Central

    Meyer, Clifford A.; He, Housheng H.; Brown, Myles; Liu, X. Shirley

    2011-01-01

    Summary: Transcription factor binding events are frequently associated with a pattern of nucleosome occupancy changes in which nucleosomes flanking the binding site increase in occupancy, while those in the vicinity of the binding site itself are displaced. Genome-wide information on enhancer proximal nucleosome occupancy can be readily acquired using ChIP-seq targeting enhancer-related histone modifications such as H3K4me2. Here, we present a software package, BINOCh that allows biologists to use such data to infer the identity of key transcription factors that regulate the response of a cell to a stimulus or determine a program of differentiation. Availability: The BINOCh open source Python package is freely available at http://liulab.dfci.harvard.edu/BINOCh under the FreeBSD license. Contact: cliff@jimmy.harvard.edu; xsliu@jimmy.harvard.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:21551136

  4. Automated adaptive inference of phenomenological dynamical models

    NASA Astrophysics Data System (ADS)

    Daniels, Bryan C.; Nemenman, Ilya

    2015-08-01

    Dynamics of complex systems is often driven by large and intricate networks of microscopic interactions, whose sheer size obfuscates understanding. With limited experimental data, many parameters of such dynamics are unknown, and thus detailed, mechanistic models risk overfitting and making faulty predictions. At the other extreme, simple ad hoc models often miss defining features of the underlying systems. Here we develop an approach that instead constructs phenomenological, coarse-grained models of network dynamics that automatically adapt their complexity to the available data. Such adaptive models produce accurate predictions even when microscopic details are unknown. The approach is computationally tractable, even for a relatively large number of dynamical variables. Using simulated data, it correctly infers the phase space structure for planetary motion, avoids overfitting in a biological signalling system and produces accurate predictions for yeast glycolysis with tens of data points and over half of the interacting species unobserved.

  5. Vitamin D deficiency in adolescents

    PubMed Central

    Soliman, Ashraf T.; De Sanctis, Vincenzo; Elalaily, Rania; Bedair, Said; Kassem, Islam

    2014-01-01

    The prevalence of severe vitamin D deficiency (VDD) in adolescents is variable but considerably high in many countries, especially in Middle-east and Southeast Asia. Different factors attribute to this deficiency including lack of sunlight exposure due to cultural dress codes and veiling or due to pigmented skin, and less time spent outdoors, because of hot weather, and lower vitamin D intake. A potent adaptation process significantly modifies the clinical presentation and therefore clinical presentations may be subtle and go unnoticed, thus making true prevalence studies difficult. Adolescents with severe VDD may present with vague manifestations including pain in weight-bearing joints, back, thighs and/or calves, difficulty in walking and/or climbing stairs, or running and muscle cramps. Adaptation includes increased parathormone (PTH) and deceased insulin-like growth factor-I (IGF-I) secretion. PTH enhances the tubular reabsorption of Ca and stimulates the kidneys to produce 1, 25-(OH) 2D3 that increases intestinal calcium absorption and dissolves the mineralized collagen matrix in bone, causing osteopenia and osteoporosis to provide enough Ca to prevent hypocalcaemia. Decreased insulin like growth factor-I (IGF-I) delays bone growth to economize calcium consumption. Radiological changes are not uncommon and include osteoporosis/osteopenia affecting long bones as well as vertebrae and ribs, bone cysts, decalcification of the metaphysis of the long bones and pseudo fractures. In severe cases pathological fractures and deformities may occur. Vitamin D treatment of adolescents with VDD differs considerably in different studies and proved to be effective in treating all clinical, biochemical, and radiological manifestations. Different treatment regiments for VDD have been discussed and presented in this mini-review for practical use. Adequate vitamin D replacement after treating VDD, improving calcium intake (milk and dairy products), encouraging adequate exposure

  6. Vitamin D deficiency in adolescents.

    PubMed

    Soliman, Ashraf T; De Sanctis, Vincenzo; Elalaily, Rania; Bedair, Said; Kassem, Islam

    2014-11-01

    The prevalence of severe vitamin D deficiency (VDD) in adolescents is variable but considerably high in many countries, especially in Middle-east and Southeast Asia. Different factors attribute to this deficiency including lack of sunlight exposure due to cultural dress codes and veiling or due to pigmented skin, and less time spent outdoors, because of hot weather, and lower vitamin D intake. A potent adaptation process significantly modifies the clinical presentation and therefore clinical presentations may be subtle and go unnoticed, thus making true prevalence studies difficult. Adolescents with severe VDD may present with vague manifestations including pain in weight-bearing joints, back, thighs and/or calves, difficulty in walking and/or climbing stairs, or running and muscle cramps. Adaptation includes increased parathormone (PTH) and deceased insulin-like growth factor-I (IGF-I) secretion. PTH enhances the tubular reabsorption of Ca and stimulates the kidneys to produce 1, 25-(OH) 2D3 that increases intestinal calcium absorption and dissolves the mineralized collagen matrix in bone, causing osteopenia and osteoporosis to provide enough Ca to prevent hypocalcaemia. Decreased insulin like growth factor-I (IGF-I) delays bone growth to economize calcium consumption. Radiological changes are not uncommon and include osteoporosis/osteopenia affecting long bones as well as vertebrae and ribs, bone cysts, decalcification of the metaphysis of the long bones and pseudo fractures. In severe cases pathological fractures and deformities may occur. Vitamin D treatment of adolescents with VDD differs considerably in different studies and proved to be effective in treating all clinical, biochemical, and radiological manifestations. Different treatment regiments for VDD have been discussed and presented in this mini-review for practical use. Adequate vitamin D replacement after treating VDD, improving calcium intake (milk and dairy products), encouraging adequate exposure

  7. Vitamin A deficiency in quail

    USGS Publications Warehouse

    Nestler, R.B.; Bailey, W.W.

    1943-01-01

    Two experiments were conducted to determine the symptoms of avitaminosis A in growing and adolescent bobwhites. Chicks from parents that have received a diet rich in vitamin A may have enough stored to carry them a week or ten days on a growing diet deficient in vitamin A before symptoms of deficiency occur. The first sign is ruffled feathering, with the wing primaries standing out from the body and drooping. Ophthalmia in one or both eyes occurs and may close the eyes completely, but this condition is not severe in all cases and may not even be noticeable. Birds show poor growth, loss of appetite, and weakness before death. Under the conditions of the experiments discussed herein, death may occur in the fourth or fifth week, and mortality is high......Postmortem examination may reveal visceral gout with thick deposits of urates on the kidneys, in the ureters, on the heart, in the proventriculus, and occasionally covering all the viscera. There may also be hemorrhage of the heart and other organs....Adolescent quail reared on a diet rich in vitamin A may be able to live through the winter on a maintenance diet low in this vitamin without showing symptoms of avitaminosis, but some individuals whose storage of vitamin A in the liver is not as great as that of others may succumb to visceral gout.....A growing mash for quail which contains sufficient vitamin A when fresh may, after a period of storage, lose enough of the vitamin to cause the characteristic symptoms of avitaminosis A to appear.

  8. Bayesian inference tools for inverse problems

    NASA Astrophysics Data System (ADS)

    Mohammad-Djafari, Ali

    2013-08-01

    In this paper, first the basics of Bayesian inference with a parametric model of the data is presented. Then, the needed extensions are given when dealing with inverse problems and in particular the linear models such as Deconvolution or image reconstruction in Computed Tomography (CT). The main point to discuss then is the prior modeling of signals and images. A classification of these priors is presented, first in separable and Markovien models and then in simple or hierarchical with hidden variables. For practical applications, we need also to consider the estimation of the hyper parameters. Finally, we see that we have to infer simultaneously on the unknowns, the hidden variables and the hyper parameters. Very often, the expression of this joint posterior law is too complex to be handled directly. Indeed, rarely we can obtain analytical solutions to any point estimators such the Maximum A posteriori (MAP) or Posterior Mean (PM). Three main tools are then can be used: Laplace approximation (LAP), Markov Chain Monte Carlo (MCMC) and Bayesian Variational Approximations (BVA). To illustrate all these aspects, we will consider a deconvolution problem where we know that the input signal is sparse and propose to use a Student-t prior for that. Then, to handle the Bayesian computations with this model, we use the property of Student-t which is modelling it via an infinite mixture of Gaussians, introducing thus hidden variables which are the variances. Then, the expression of the joint posterior of the input signal samples, the hidden variables (which are here the inverse variances of those samples) and the hyper-parameters of the problem (for example the variance of the noise) is given. From this point, we will present the joint maximization by alternate optimization and the three possible approximation methods. Finally, the proposed methodology is applied in different applications such as mass spectrometry, spectrum estimation of quasi periodic biological signals and

  9. Nuclear Forensic Inferences Using Iterative Multidimensional Statistics

    SciTech Connect

    Robel, M; Kristo, M J; Heller, M A

    2009-06-09

    Nuclear forensics involves the analysis of interdicted nuclear material for specific material characteristics (referred to as 'signatures') that imply specific geographical locations, production processes, culprit intentions, etc. Predictive signatures rely on expert knowledge of physics, chemistry, and engineering to develop inferences from these material characteristics. Comparative signatures, on the other hand, rely on comparison of the material characteristics of the interdicted sample (the 'questioned sample' in FBI parlance) with those of a set of known samples. In the ideal case, the set of known samples would be a comprehensive nuclear forensics database, a database which does not currently exist. In fact, our ability to analyze interdicted samples and produce an extensive list of precise materials characteristics far exceeds our ability to interpret the results. Therefore, as we seek to develop the extensive databases necessary for nuclear forensics, we must also develop the methods necessary to produce the necessary inferences from comparison of our analytical results with these large, multidimensional sets of data. In the work reported here, we used a large, multidimensional dataset of results from quality control analyses of uranium ore concentrate (UOC, sometimes called 'yellowcake'). We have found that traditional multidimensional techniques, such as principal components analysis (PCA), are especially useful for understanding such datasets and drawing relevant conclusions. In particular, we have developed an iterative partial least squares-discriminant analysis (PLS-DA) procedure that has proven especially adept at identifying the production location of unknown UOC samples. By removing classes which fell far outside the initial decision boundary, and then rebuilding the PLS-DA model, we have consistently produced better and more definitive attributions than with a single pass classification approach. Performance of the iterative PLS-DA method

  10. Network geometry inference using common neighbors

    NASA Astrophysics Data System (ADS)

    Papadopoulos, Fragkiskos; Aldecoa, Rodrigo; Krioukov, Dmitri

    2015-08-01

    We introduce and explore a method for inferring hidden geometric coordinates of nodes in complex networks based on the number of common neighbors between the nodes. We compare this approach to the HyperMap method, which is based only on the connections (and disconnections) between the nodes, i.e., on the links that the nodes have (or do not have). We find that for high degree nodes, the common-neighbors approach yields a more accurate inference than the link-based method, unless heuristic periodic adjustments (or "correction steps") are used in the latter. The common-neighbors approach is computationally intensive, requiring O (t4) running time to map a network of t nodes, versus O (t3) in the link-based method. But we also develop a hybrid method with O (t3) running time, which combines the common-neighbors and link-based approaches, and we explore a heuristic that reduces its running time further to O (t2) , without significant reduction in the mapping accuracy. We apply this method to the autonomous systems (ASs) Internet, and we reveal how soft communities of ASs evolve over time in the similarity space. We further demonstrate the method's predictive power by forecasting future links between ASs. Taken altogether, our results advance our understanding of how to efficiently and accurately map real networks to their latent geometric spaces, which is an important necessary step toward understanding the laws that govern the dynamics of nodes in these spaces, and the fine-grained dynamics of network connections.

  11. Network geometry inference using common neighbors.

    PubMed

    Papadopoulos, Fragkiskos; Aldecoa, Rodrigo; Krioukov, Dmitri

    2015-08-01

    We introduce and explore a method for inferring hidden geometric coordinates of nodes in complex networks based on the number of common neighbors between the nodes. We compare this approach to the HyperMap method, which is based only on the connections (and disconnections) between the nodes, i.e., on the links that the nodes have (or do not have). We find that for high degree nodes, the common-neighbors approach yields a more accurate inference than the link-based method, unless heuristic periodic adjustments (or "correction steps") are used in the latter. The common-neighbors approach is computationally intensive, requiring O(t4) running time to map a network of t nodes, versus O(t3) in the link-based method. But we also develop a hybrid method with O(t3) running time, which combines the common-neighbors and link-based approaches, and we explore a heuristic that reduces its running time further to O(t2), without significant reduction in the mapping accuracy. We apply this method to the autonomous systems (ASs) Internet, and we reveal how soft communities of ASs evolve over time in the similarity space. We further demonstrate the method's predictive power by forecasting future links between ASs. Taken altogether, our results advance our understanding of how to efficiently and accurately map real networks to their latent geometric spaces, which is an important necessary step toward understanding the laws that govern the dynamics of nodes in these spaces, and the fine-grained dynamics of network connections. PMID:26382454

  12. Neural representation of probabilities for Bayesian inference.

    PubMed

    Rich, Dylan; Cazettes, Fanny; Wang, Yunyan; Peña, José Luis; Fischer, Brian J

    2015-04-01

    Bayesian models are often successful in describing perception and behavior, but the neural representation of probabilities remains in question. There are several distinct proposals for the neural representation of probabilities, but they have not been directly compared in an example system. Here we consider three models: a non-uniform population code where the stimulus-driven activity and distribution of preferred stimuli in the population represent a likelihood function and a prior, respectively; the sampling hypothesis which proposes that the stimulus-driven activity over time represents a posterior probability and that the spontaneous activity represents a prior; and the class of models which propose that a population of neurons represents a posterior probability in a distributed code. It has been shown that the non-uniform population code model matches the representation of auditory space generated in the owl's external nucleus of the inferior colliculus (ICx). However, the alternative models have not been tested, nor have the three models been directly compared in any system. Here we tested the three models in the owl's ICx. We found that spontaneous firing rate and the average stimulus-driven response of these neurons were not consistent with predictions of the sampling hypothesis. We also found that neural activity in ICx under varying levels of sensory noise did not reflect a posterior probability. On the other hand, the responses of ICx neurons were consistent with the non-uniform population code model. We further show that Bayesian inference can be implemented in the non-uniform population code model using one spike per neuron when the population is large and is thus able to support the rapid inference that is necessary for sound localization. PMID:25561333

  13. Pathway network inference from gene expression data

    PubMed Central

    2014-01-01

    Background The development of high-throughput omics technologies enabled genome-wide measurements of the activity of cellular elements and provides the analytical resources for the progress of the Systems Biology discipline. Analysis and interpretation of gene expression data has evolved from the gene to the pathway and interaction level, i.e. from the detection of differentially expressed genes, to the establishment of gene interaction networks and the identification of enriched functional categories. Still, the understanding of biological systems requires a further level of analysis that addresses the characterization of the interaction between functional modules. Results We present a novel computational methodology to study the functional interconnections among the molecular elements of a biological system. The PANA approach uses high-throughput genomics measurements and a functional annotation scheme to extract an activity profile from each functional block -or pathway- followed by machine-learning methods to infer the relationships between these functional profiles. The result is a global, interconnected network of pathways that represents the functional cross-talk within the molecular system. We have applied this approach to describe the functional transcriptional connections during the yeast cell cycle and to identify pathways that change their connectivity in a disease condition using an Alzheimer example. Conclusions PANA is a useful tool to deepen in our understanding of the functional interdependences that operate within complex biological systems. We show the approach is algorithmically consistent and the inferred network is well supported by the available functional data. The method allows the dissection of the molecular basis of the functional connections and we describe the different regulatory mechanisms that explain the network's topology obtained for the yeast cell cycle data. PMID:25032889

  14. Active Inference, homeostatic regulation and adaptive behavioural control

    PubMed Central

    Pezzulo, Giovanni; Rigoli, Francesco; Friston, Karl

    2015-01-01

    We review a theory of homeostatic regulation and adaptive behavioural control within the Active Inference framework. Our aim is to connect two research streams that are usually considered independently; namely, Active Inference and associative learning theories of animal behaviour. The former uses a probabilistic (Bayesian) formulation of perception and action, while the latter calls on multiple (Pavlovian, habitual, goal-directed) processes for homeostatic and behavioural control. We offer a synthesis these classical processes and cast them as successive hierarchical contextualisations of sensorimotor constructs, using the generative models that underpin Active Inference. This dissolves any apparent mechanistic distinction between the optimization processes that mediate classical control or learning. Furthermore, we generalize the scope of Active Inference by emphasizing interoceptive inference and homeostatic regulation. The ensuing homeostatic (or allostatic) perspective provides an intuitive explanation for how priors act as drives or goals to enslave action, and emphasises the embodied nature of inference. PMID:26365173

  15. Active Inference, homeostatic regulation and adaptive behavioural control.

    PubMed

    Pezzulo, Giovanni; Rigoli, Francesco; Friston, Karl

    2015-11-01

    We review a theory of homeostatic regulation and adaptive behavioural control within the Active Inference framework. Our aim is to connect two research streams that are usually considered independently; namely, Active Inference and associative learning theories of animal behaviour. The former uses a probabilistic (Bayesian) formulation of perception and action, while the latter calls on multiple (Pavlovian, habitual, goal-directed) processes for homeostatic and behavioural control. We offer a synthesis these classical processes and cast them as successive hierarchical contextualisations of sensorimotor constructs, using the generative models that underpin Active Inference. This dissolves any apparent mechanistic distinction between the optimization processes that mediate classical control or learning. Furthermore, we generalize the scope of Active Inference by emphasizing interoceptive inference and homeostatic regulation. The ensuing homeostatic (or allostatic) perspective provides an intuitive explanation for how priors act as drives or goals to enslave action, and emphasises the embodied nature of inference. PMID:26365173

  16. Interplanetary magnetic sector polarity inferred from polar geomagnetic field observations

    NASA Technical Reports Server (NTRS)

    Friis-Christensen, E.; Lassen, K.; Wilcox, J. M.; Gonzalez, W.; Colburn, D. S.

    1971-01-01

    In order to infer the interplanetary sector polarity from polar geomagnetic field diurnal variations, measurements were carried out at Godhavn and Thule (Denmark) Geomagnetic Observatories. The inferred interplanetary sector polarity was compared with the polarity observed at the same time by Explorer 33 and 35 magnetometers. It is shown that the polarity (toward or away from the sun) of the interplanetary magnetic field can be reliably inferred from observations of the polar cap geomagnetic fields.

  17. How common is vitamin B12 deficiency?

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In considering the vitamin B-12 fortification of flour, it is important to know who is at risk of vitamin B-12 deficiency and whether those individuals would benefit from flour fortification.This article reviews current knowledge of the prevalence and causes of vitamin B-12 deficiency and considers ...

  18. [Factor VII deficiency revealed by intracranial hemorrhage].

    PubMed

    Sfaihi Ben Mansour, L; Thabet, A; Aloulou, H; Turki, H; Chabchoub, I; Mhiri, F; Mnif, Z; Ben Ali, H; Kammoun, T; Hachicha, M

    2009-07-01

    Constitutional factor VII deficiency is a hereditary disease with recessive autosomic transmission. Its incidence is estimated to be 1/1,000,000 in the general population. We report a case of severe factor VII deficiency in infancy revealed by an intracranial hemorrhage in a 2-month-old infant. We describe the clinical, biological and therapeutic characteristics of this disease. PMID:19409767

  19. Growth Hormone Deficiency, Brain Development, and Intelligence

    ERIC Educational Resources Information Center

    Meyer-Bahlburg, Heino F. L.; And Others

    1978-01-01

    Available from: American Medical Association, 535 N. Dearborn Street, Chicago, Illinois 60610. In order to determine what effect, if any, growth hormone (GH) has on human brain development, 29 patients (mean age 11.7 years) with GH deficiency were selected according to the following criteria: no evidence of reversible GH deficiency, onset of…

  20. 30 CFR 57.5015 - Oxygen deficiency.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 30 Mineral Resources 1 2012-07-01 2012-07-01 false Oxygen deficiency. 57.5015 Section 57.5015..., Physical Agents, and Diesel Particulate Matter Air Quality-Underground Only § 57.5015 Oxygen deficiency. Air in all active workings shall contain at least 19.5 volume percent oxygen....

  1. 30 CFR 57.5015 - Oxygen deficiency.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 30 Mineral Resources 1 2014-07-01 2014-07-01 false Oxygen deficiency. 57.5015 Section 57.5015..., Physical Agents, and Diesel Particulate Matter Air Quality-Underground Only § 57.5015 Oxygen deficiency. Air in all active workings shall contain at least 19.5 volume percent oxygen....

  2. 30 CFR 57.5015 - Oxygen deficiency.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 30 Mineral Resources 1 2010-07-01 2010-07-01 false Oxygen deficiency. 57.5015 Section 57.5015..., Physical Agents, and Diesel Particulate Matter Air Quality-Underground Only § 57.5015 Oxygen deficiency. Air in all active workings shall contain at least 19.5 volume percent oxygen....

  3. 30 CFR 57.5015 - Oxygen deficiency.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 30 Mineral Resources 1 2011-07-01 2011-07-01 false Oxygen deficiency. 57.5015 Section 57.5015..., Physical Agents, and Diesel Particulate Matter Air Quality-Underground Only § 57.5015 Oxygen deficiency. Air in all active workings shall contain at least 19.5 volume percent oxygen....

  4. 30 CFR 57.5015 - Oxygen deficiency.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 30 Mineral Resources 1 2013-07-01 2013-07-01 false Oxygen deficiency. 57.5015 Section 57.5015..., Physical Agents, and Diesel Particulate Matter Air Quality-Underground Only § 57.5015 Oxygen deficiency. Air in all active workings shall contain at least 19.5 volume percent oxygen....

  5. 36 CFR 1120.26 - Deficient descriptions.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 36 Parks, Forests, and Public Property 3 2010-07-01 2010-07-01 false Deficient descriptions. 1120.26 Section 1120.26 Parks, Forests, and Public Property ARCHITECTURAL AND TRANSPORTATION BARRIERS COMPLIANCE BOARD PUBLIC AVAILABILITY OF INFORMATION Information Available Upon Request § 1120.26 Deficient descriptions. (a) If the description of...

  6. Genetics Home Reference: triosephosphate isomerase deficiency

    MedlinePlus

    ... of triosephosphate isomerase deficiency. Eur J Haematol. 2011 Mar;86(3):265-7. doi: 10.1111/j.1600-0609.2010.01484.x. Citation on PubMed Orosz F, Oláh J, Ovádi J. Triosephosphate isomerase deficiency: facts and doubts. IUBMB Life. 2006 Dec;58(12):703-15. Review. Citation ...

  7. Academic Deficiency: Student Experiences of Institutional Labeling

    ERIC Educational Resources Information Center

    Barouch-Gilbert, Abraham

    2015-01-01

    Limited existing research examines how undergraduate students in the United States experience the process of being identified as deficient due to their academic performance. The purpose of this phenomenological study was to explore the lived experiences of college students on academic probation who were labeled academically deficient. Students…

  8. An update on serine deficiency disorders.

    PubMed

    van der Crabben, S N; Verhoeven-Duif, N M; Brilstra, E H; Van Maldergem, L; Coskun, T; Rubio-Gozalbo, E; Berger, R; de Koning, T J

    2013-07-01

    Serine deficiency disorders are caused by a defect in one of the three synthesising enzymes of the L-serine biosynthesis pathway. Serine deficiency disorders give rise to a neurological phenotype with psychomotor retardation, microcephaly and seizures in newborns and children or progressive polyneuropathy in adult patients. There are three defects that cause serine deficiency of which 3-phosphoglycerate dehydrogenase (3-PGDH) deficiency, the defect affecting the first step in the pathway, has been reported most frequently. The other two disorders in L-serine biosynthesis phosphoserine aminotransferase (PSAT) deficiency and phosphoserine phosphatase (PSP) deficiency have been reported only in a limited number of patients. The biochemical hallmarks of all three disorders are low concentrations of serine in cerebrospinal fluid and plasma. Prompt recognition of affected patients is important, since serine deficiency disorders are treatable causes of neurometabolic disorders. The use of age-related reference values for serine in CSF and plasma can be of great help in establishing a correct diagnosis of serine deficiency, in particular in newborns and young children. PMID:23463425

  9. Selective deficiency of IgA

    MedlinePlus

    Consider genetic counseling if you have a family history of selective IgA deficiency and you plan to have children. If ... Genetic counseling may be of value to prospective parents with a family history of selective IgA deficiency.

  10. Duodenal Amyloidosis Masquerading as Iron Deficiency Anemia

    PubMed Central

    Hurairah, Abu

    2016-01-01

    The present study is a unique illustration of duodenal amyloidosis initially manifesting with iron deficiency anemia. It underscores the importance of clinical suspicion of amyloidosis while performing upper gastrointestinal endoscopy with a biopsy to establish the definite diagnosis in patients with unexplained iron deficiency anemia. PMID:27625911

  11. Genetics Home Reference: pyruvate kinase deficiency

    MedlinePlus

    ... National (UK) Information Centre for Metabolic Diseases National Organization for Rare Disorders (NORD): Pyruvate Kinase Deficiency Genetic Testing Registry (1 link) Pyruvate kinase deficiency of red cells Scientific articles on PubMed (1 link) PubMed OMIM (1 link) ...

  12. Acquired Zinc Deficiency in an Adult Female

    PubMed Central

    Saritha, Mohanan; Gupta, Divya; Chandrashekar, Laxmisha; Thappa, Devinder M; Rajesh, Nachiappa G

    2012-01-01

    Acrodermatitis enteropathica is an autosomal recessive inherited disorder of zinc absorption. Acquired cases are reported occasionally in patients with eating disorders or Crohn's disease. We report a 24-year-old housewife with acquired isolated severe zinc deficiency with no other comorbidities to highlight the rare occurrence of isolated nutritional zinc deficiency in an otherwise normal patient. PMID:23248371

  13. 33 CFR 154.1070 - Deficiencies.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 33 Navigation and Navigable Waters 2 2010-07-01 2010-07-01 false Deficiencies. 154.1070 Section 154.1070 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) POLLUTION FACILITIES TRANSFERRING OIL OR HAZARDOUS MATERIAL IN BULK Response Plans for Oil Facilities § 154.1070 Deficiencies. (a) The cognizant COTP...

  14. 24 CFR 203.369 - Deficiency judgments.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... State law to obtain a deficiency judgment. (b) Mortgages insured before March 28, 1988. For mortgages... 24 Housing and Urban Development 2 2010-04-01 2010-04-01 false Deficiency judgments. 203.369... SINGLE FAMILY MORTGAGE INSURANCE Contract Rights and Obligations Claim Procedure § 203.369...

  15. 37 CFR 2.185 - Correcting deficiencies in renewal application.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... the deficiency surcharge required by section 9(a) of the Act and § 2.6. (b) If the renewal application..., deficiencies may be corrected before the expiration date of the registration without paying a deficiency... deficiency surcharge required by section 9(a) of the Act and § 2.6. (2) Correcting deficiencies in...

  16. Inferring word meanings by assuming that speakers are informative.

    PubMed

    Frank, Michael C; Goodman, Noah D

    2014-12-01

    Language comprehension is more than a process of decoding the literal meaning of a speaker's utterance. Instead, by making the assumption that speakers choose their words to be informative in context, listeners routinely make pragmatic inferences that go beyond the linguistic data. If language learners make these same assumptions, they should be able to infer word meanings in otherwise ambiguous situations. We use probabilistic tools to formalize these kinds of informativeness inferences-extending a model of pragmatic language comprehension to the acquisition setting-and present four experiments whose data suggest that preschool children can use informativeness to infer word meanings and that adult judgments track quantitatively with informativeness. PMID:25238461

  17. Inferring ancestry from population genomic data and its applications

    PubMed Central

    Padhukasahasram, Badri

    2014-01-01

    Ancestry inference is a frequently encountered problem and has many applications such as forensic analyses, genetic association studies, and personal genomics. The main goal of ancestry inference is to identify an individual’s population of origin based on our knowledge of natural populations. Because both self-reported ancestry in humans or the sampling location of an organism can be inaccurate for this purpose, the use of genetic markers can facilitate accurate and reliable inference of an individual’s ancestral origins. At a higher level, there are two different paradigms in ancestry inference: global ancestry inference which tries to compute the genome-wide average of the population contributions and local ancestry inference which tries to identify the regional ancestry of a genomic segment. In this mini review, I describe the numerous approaches that are currently available for both kinds of ancestry inference from population genomic datasets. I first describe the general ideas underlying such inference methods and their relationship to one another. Then, I describe practical applications in which inference of ancestry has proven useful. Lastly, I discuss challenges and directions for future research work in this area. PMID:25071832

  18. Thiamin Deficiency in People with Obesity12

    PubMed Central

    Kerns, Jennifer C; Arundel, Cherinne; Chawla, Lakhmir S

    2015-01-01

    Although obesity has been viewed traditionally as a disease of excess nutrition, evidence suggests that it may also be a disease of malnutrition. Specifically, thiamin deficiency was found in 15.5–29% of obese patients seeking bariatric surgery. It can present with vague signs and symptoms and is often overlooked in patients without alcohol use disorders. This review explores the relatively new discovery of high rates of thiamin deficiency in certain populations of people with obesity, including the effects of thiamin deficiency and potential underlying mechanisms of deficiency in people with obesity. The 2 observational studies that examined the prevalence in preoperative bariatric surgery patients and gaps in our current knowledge (including the prevalence of thiamin deficiency in the general obese population and whether the current RDA for thiamin meets the metabolic needs of overweight or obese adults) are reviewed. Suggestions for future areas of research are included. PMID:25770253

  19. [Vitamin B12 deficiency in the elderly].

    PubMed

    Leischker, A H; Kolb, G F

    2015-01-01

    The prevalence of vitamin B12 deficiency increases with age. Patients with dementia and spouses of patients with dementia are at special risk for the development of vitamin B12 deficiency. In a normal diet this vitamin is present only in animal source foods; therefore, vegans frequently develop vitamin B12 deficiency if not using supplements or foods fortified with cobalamin. Apart from dementia, most of these manifestations are completely reversible under correct therapy; therefore it is crucial to identify and to treat even atypical presentations of vitamin B12 deficiency as early as possible. This article deals with the physiology and pathophysiology of vitamin B12 metabolism. A practice-oriented algorithm which also considers health economic aspects for a rational laboratory diagnosis of vitamin B12 deficiency is presented. In cases with severe neurological symptoms, therapy should be parenteral, especially initially. For parenteral treatment, hydroxocobalamin is the drug of choice. PMID:25586321

  20. Molecular diagnosis of coenzyme Q10 deficiency.

    PubMed

    Yubero, Delia; Montero, Raquel; Armstrong, Judith; Espinós, Carmen; Palau, Francesc; Santos-Ocaña, Carlos; Salviati, Leonardo; Navas, Placido; Artuch, Rafael

    2015-01-01

    Coenzyme Q10 (CoQ) deficiency syndromes comprise a growing number of neurological and extraneurological disorders. Primary-genetic but also secondary CoQ deficiencies have been reported. The biochemical determination of CoQ is a good tool for the rapid identification of CoQ deficiencies but does not allow the selection of candidate genes for molecular diagnosis. Moreover, the metabolic pathway for CoQ synthesis is an intricate and not well-understood process, where a large number of genes are implicated. Thus, only next-generation sequencing techniques (either genetic panels of whole-exome and -genome sequencing) are at present appropriate for a rapid and realistic molecular diagnosis of these syndromes. The potential treatability of CoQ deficiency strongly supports the necessity of a rapid molecular characterization of patients, since primary CoQ deficiencies may respond well to CoQ treatment. PMID:26144946

  1. The Probabilistic Convolution Tree: Efficient Exact Bayesian Inference for Faster LC-MS/MS Protein Inference

    PubMed Central

    Serang, Oliver

    2014-01-01

    Exact Bayesian inference can sometimes be performed efficiently for special cases where a function has commutative and associative symmetry of its inputs (called “causal independence”). For this reason, it is desirable to exploit such symmetry on big data sets. Here we present a method to exploit a general form of this symmetry on probabilistic adder nodes by transforming those probabilistic adder nodes into a probabilistic convolution tree with which dynamic programming computes exact probabilities. A substantial speedup is demonstrated using an illustration example that can arise when identifying splice forms with bottom-up mass spectrometry-based proteomics. On this example, even state-of-the-art exact inference algorithms require a runtime more than exponential in the number of splice forms considered. By using the probabilistic convolution tree, we reduce the runtime to and the space to where is the number of variables joined by an additive or cardinal operator. This approach, which can also be used with junction tree inference, is applicable to graphs with arbitrary dependency on counting variables or cardinalities and can be used on diverse problems and fields like forward error correcting codes, elemental decomposition, and spectral demixing. The approach also trivially generalizes to multiple dimensions. PMID:24626234

  2. Impact of Prematurity and Perinatal Antibiotics on the Developing Intestinal Microbiota: A Functional Inference Study

    PubMed Central

    Arboleya, Silvia; Sánchez, Borja; Solís, Gonzalo; Fernández, Nuria; Suárez, Marta; Hernández-Barranco, Ana M.; Milani, Christian; Margolles, Abelardo; de los Reyes-Gavilán, Clara G.; Ventura, Marco; Gueimonde, Miguel

    2016-01-01

    Background: The microbial colonization of the neonatal gut provides a critical stimulus for normal maturation and development. This process of early microbiota establishment, known to be affected by several factors, constitutes an important determinant for later health. Methods: We studied the establishment of the microbiota in preterm and full-term infants and the impact of perinatal antibiotics upon this process in premature babies. To this end, 16S rRNA gene sequence-based microbiota assessment was performed at phylum level and functional inference analyses were conducted. Moreover, the levels of the main intestinal microbial metabolites, the short-chain fatty acids (SCFA) acetate, propionate and butyrate, were measured by Gas-Chromatography Flame ionization/Mass spectrometry detection. Results: Prematurity affects microbiota composition at phylum level, leading to increases of Proteobacteria and reduction of other intestinal microorganisms. Perinatal antibiotic use further affected the microbiota of the preterm infant. These changes involved a concomitant alteration in the levels of intestinal SCFA. Moreover, functional inference analyses allowed for identifying metabolic pathways potentially affected by prematurity and perinatal antibiotics use. Conclusion: A deficiency or delay in the establishment of normal microbiota function seems to be present in preterm infants. Perinatal antibiotic use, such as intrapartum prophylaxis, affected the early life microbiota establishment in preterm newborns, which may have consequences for later health. PMID:27136545

  3. Folate deficiency affects histone methylation.

    PubMed

    Garcia, Benjamin A; Luka, Zigmund; Loukachevitch, Lioudmila V; Bhanu, Natarajan V; Wagner, Conrad

    2016-03-01

    that the bound THF serves to protect the FAD class of histone demethylases from the destructive effects of formaldehyde generation by formation of 5,10-methylene-THF. We present pilot data showing that decreased folate in livers as a result of dietary folate deficiency is associated with increased levels of methylated lysine 4 of histone 3. This can be a result of decreased LSD1 activity resulting from the decreased folate available to scavenge the formaldehyde produced at the active site caused by the folate deficiency. Because LSD1 can regulate gene expression this suggests that folate may play a more important role than simply serving as a carrier of one-carbon units and be a factor in other diseases associated with low folate. PMID:26880641

  4. Infections Revealing Complement Deficiency in Adults

    PubMed Central

    Audemard-Verger, A.; Descloux, E.; Ponard, D.; Deroux, A.; Fantin, B.; Fieschi, C.; John, M.; Bouldouyre, A.; Karkowsi, L.; Moulis, G.; Auvinet, H.; Valla, F.; Lechiche, C.; Davido, B.; Martinot, M.; Biron, C.; Lucht, F.; Asseray, N.; Froissart, A.; Buzelé, R.; Perlat, A.; Boutboul, D.; Fremeaux-Bacchi, V.; Isnard, S.; Bienvenu, B.

    2016-01-01

    Abstract Complement system is a part of innate immunity, its main function is to protect human from bacterial infection. As genetic disorders, complement deficiencies are often diagnosed in pediatric population. However, complement deficiencies can also be revealed in adults but have been poorly investigated. Herein, we describe a case series of infections revealing complement deficiency in adults to study clinical spectrum and management of complement deficiencies. A nationwide retrospective study was conducted in French university and general hospitals in departments of internal medicine, infectious diseases enrolling patients older than 15 years old who had presented at least one infection leading to a complement deficiency diagnosis. Forty-one patients included between 2002 and 2015 in 19 different departments were enrolled in this study. The male-to-female ratio was 1.3 and the mean age at diagnosis was 28 ± 14 (15–67) years. The main clinical feature was Neisseria meningitidis meningitis 75% (n = 31/41) often involving rare serotype: Y (n = 9) and W 135 (n = 7). The main complement deficiency observed was the common final pathway deficiency 83% (n = 34/41). Half of the cohort displayed severe sepsis or septic shock at diagnosis (n = 22/41) but no patient died. No patient had family history of complement deficiency. The mean follow-up was 1.15 ± 1.95 (0.1–10) years. Half of the patients had already suffered from at least one infection before diagnosis of complement deficiency: meningitis (n = 13), pneumonia (n = 4), fulminans purpura (n = 1), or recurrent otitis (n = 1). Near one-third (n = 10/39) had received prophylactic antibiotics (cotrimoxazole or penicillin) after diagnosis of complement deficiency. The vaccination coverage rate, at the end of the follow-up, for N meningitidis, Streptococcus pneumonia, and Haemophilius influenzae were, respectively, 90% (n = 33/37), 47% (n = 17/36), and 35

  5. Genetics Home Reference: alpha-methylacyl-CoA racemase deficiency

    MedlinePlus

    ... Me Understand Genetics Home Health Conditions AMACR deficiency alpha-methylacyl-CoA racemase deficiency Enable Javascript to view ... boxes. Download PDF Open All Close All Description Alpha-methylacyl-CoA racemase (AMACR) deficiency is a disorder ...

  6. Genetics Home Reference: aromatic l-amino acid decarboxylase deficiency

    MedlinePlus

    ... aromatic l-amino acid decarboxylase deficiency aromatic l-amino acid decarboxylase deficiency Enable Javascript to view the expand/ ... PDF Open All Close All Description Aromatic l-amino acid decarboxylase (AADC) deficiency is an inherited disorder that ...

  7. Genetics Home Reference: iron-refractory iron deficiency anemia

    MedlinePlus

    ... refractory iron deficiency anemia iron-refractory iron deficiency anemia Enable Javascript to view the expand/collapse boxes. ... All Close All Description Iron-refractory iron deficiency anemia is one of many types of anemia , which ...

  8. Genetics Home Reference: leukocyte adhesion deficiency type 1

    MedlinePlus

    ... adhesion deficiency type 1 leukocyte adhesion deficiency type 1 Enable Javascript to view the expand/collapse boxes. ... All Close All Description Leukocyte adhesion deficiency type 1 is a disorder that causes the immune system ...

  9. Genetics Home Reference: D-bifunctional protein deficiency

    MedlinePlus

    ... Genetics Home Health Conditions D-bifunctional protein deficiency D-bifunctional protein deficiency Enable Javascript to view the ... boxes. Download PDF Open All Close All Description D-bifunctional protein deficiency is a disorder that causes ...

  10. Genetics Home Reference: congenital sucrase-isomaltase deficiency

    MedlinePlus

    ... and other compounds made from these sugar molecules (carbohydrates). Congenital sucrase-isomaltase deficiency usually becomes apparent after ... isomaltase deficiency, congenital Merck Manual for Healthcare Professionals: Carbohydrate ... Congenital sucrase-isomaltase deficiency The American ...

  11. Ensembles of Spiking Neurons with Noise Support Optimal Probabilistic Inference in a Dynamically Changing Environment

    PubMed Central

    Legenstein, Robert; Maass, Wolfgang

    2014-01-01

    It has recently been shown that networks of spiking neurons with noise can emulate simple forms of probabilistic inference through “neural sampling”, i.e., by treating spikes as samples from a probability distribution of network states that is encoded in the network. Deficiencies of the existing model are its reliance on single neurons for sampling from each random variable, and the resulting limitation in representing quickly varying probabilistic information. We show that both deficiencies can be overcome by moving to a biologically more realistic encoding of each salient random variable through the stochastic firing activity of an ensemble of neurons. The resulting model demonstrates that networks of spiking neurons with noise can easily track and carry out basic computational operations on rapidly varying probability distributions, such as the odds of getting rewarded for a specific behavior. We demonstrate the viability of this new approach towards neural coding and computation, which makes use of the inherent parallelism of generic neural circuits, by showing that this model can explain experimentally observed firing activity of cortical neurons for a variety of tasks that require rapid temporal integration of sensory information. PMID:25340749

  12. Expression profiling in progressive stages of fumarate-hydratase deficiency: the contribution of metabolic changes to tumorigenesis.

    PubMed

    Ashrafian, Houman; O'Flaherty, Linda; Adam, Julie; Steeples, Violetta; Chung, Yuen-Li; East, Phil; Vanharanta, Sakari; Lehtonen, Heli; Nye, Emma; Hatipoglu, Emine; Miranda, Melroy; Howarth, Kimberley; Shukla, Deepa; Troy, Helen; Griffiths, John; Spencer-Dene, Bradley; Yusuf, Mohammed; Volpi, Emanuela; Maxwell, Patrick H; Stamp, Gordon; Poulsom, Richard; Pugh, Christopher W; Costa, Barbara; Bardella, Chiara; Di Renzo, Maria Flavia; Kotlikoff, Michael I; Launonen, Virpi; Aaltonen, Lauri; El-Bahrawy, Mona; Tomlinson, Ian; Pollard, Patrick J

    2010-11-15

    Hereditary leiomyomatosis and renal cell carcinoma (HLRCC) is caused by mutations in the Krebs cycle enzyme fumarate hydratase (FH). It has been proposed that "pseudohypoxic" stabilization of hypoxia-inducible factor-α (HIF-α) by fumarate accumulation contributes to tumorigenesis in HLRCC. We hypothesized that an additional direct consequence of FH deficiency is the establishment of a biosynthetic milieu. To investigate this hypothesis, we isolated primary mouse embryonic fibroblast (MEF) lines from Fh1-deficient mice. As predicted, these MEFs upregulated Hif-1α and HIF target genes directly as a result of FH deficiency. In addition, detailed metabolic assessment of these MEFs confirmed their dependence on glycolysis, and an elevated rate of lactate efflux, associated with the upregulation of glycolytic enzymes known to be associated with tumorigenesis. Correspondingly, Fh1-deficient benign murine renal cysts and an advanced human HLRCC-related renal cell carcinoma manifested a prominent and progressive increase in the expression of HIF-α target genes and in genes known to be relevant to tumorigenesis and metastasis. In accord with our hypothesis, in a variety of different FH-deficient tissues, including a novel murine model of Fh1-deficient smooth muscle, we show a striking and progressive upregulation of a tumorigenic metabolic profile, as manifested by increased PKM2 and LDHA protein. Based on the models assessed herein, we infer that that FH deficiency compels cells to adopt an early, reversible, and progressive protumorigenic metabolic milieu that is reminiscent of that driving the Warburg effect. Targets identified in these novel and diverse FH-deficient models represent excellent potential candidates for further mechanistic investigation and therapeutic metabolic manipulation in tumors. PMID:20978192

  13. Leptin deficiency in maltreated children

    PubMed Central

    Danese, A; Dove, R; Belsky, D W; Henchy, J; Williams, B; Ambler, A; Arseneault, L

    2014-01-01

    Consistent with findings from experimental research in nonhuman primates exposed to early-life stress, children exposed to maltreatment are at high risk of detrimental physical health conditions, such as obesity and systemic inflammation. Because leptin is a key molecule involved in the regulation of both energy balance and immunity, we investigated abnormalities in leptin physiology among maltreated children. We measured leptin, body mass index and C-reactive protein in 170 12-year-old children members of the Environmental-Risk Longitudinal Twin Study, for whom we had prospectively-collected information on maltreatment exposure. We found that maltreated children exhibited blunted elevation in leptin levels in relation to increasing levels of physiological stimuli, adiposity and inflammation, compared with a group of non-maltreated children matched for gender, zygosity and socioeconomic status. These findings were also independent of key potential artifacts and confounders, such as time of day at sample collection, history of food insecurity, pubertal maturation and depressive symptoms. Furthermore, using birth weight as a proxy measure for leptin, we found that physiological abnormalities were presumably not present at birth in children who went on to be maltreated but only emerged over the course of childhood, after maltreatment exposure. Leptin deficiency may contribute to onset, persistence and progression of physical health problems in maltreated children. PMID:25247591

  14. Cernunnos deficiency: a case report.

    PubMed

    Turul, T; Tezcan, I; Sanal, O

    2011-01-01

    B cell-negative severe combined immunodeficiency (SCID) is caused by molecules involved in the variable (diversity) joining (V[D]J) recombination process. Four genes involved in the nonhomologous end joining pathway--Artemis, DNA-PKcs, DNA ligase 4, and Cernunnos--are involved in B cell-negative radiosensitive SCID. Deficiencies in DNA ligase 4 and the recently described Cernunnos gene result in microcephaly, growth retardation, and typical bird-like facies. Lymphopenia and hypogammaglobulinemia with normal or elevated immunoglobulin (Ig) M levels indicate a defect in V(D)J recombination. We present a case with recurrent postnatal pulmonary infections leading to chronic lung disease, disseminated molluscum contagiosum, lymphopenia, low IgG, IgA and normal IgM levels. Our patient had phenotypic features such as microcephaly and severe growth retardation. Clinical presentation in patients with the B cell-negative subtype ranges from SCID to atypical combined immunodeficiency, occasionally associated with autoimmune manifestations and cytomegalovirus infection. Our patient survived beyond infancy with combined immunodeficiency and no autoimmune manifestations. PMID:21721379

  15. Testosterone deficiency and cardiovascular mortality

    PubMed Central

    Morgentaler, Abraham

    2015-01-01

    New concerns have been raised regarding cardiovascular (CV) risks with testosterone (T) therapy (TTh). These concerns are based primarily on two widely reported retrospective studies. However, methodological flaws and data errors invalidate both studies as credible evidence of risk. One showed reduced adverse events by half in T-treated men but reversed this result using an unproven statistical approach. The authors subsequently acknowledged serious data errors including nearly 10% contamination of the dataset by women. The second study mistakenly used the rate of T prescriptions written by healthcare providers to men with recent myocardial infarction (MI) as a proxy for the naturally occurring rate of MI. Numerous studies suggest T is beneficial, including decreased mortality in association with TTh, reduced MI rate with TTh in men with the greatest MI risk prognosis, and reduced CV and overall mortality with higher serum levels of endogenous T. Randomized controlled trials have demonstrated benefits of TTh in men with coronary artery disease and congestive heart failure. Improvement in CV risk factors such as fat mass and glycemic control have been repeatedly demonstrated in T-deficient men treated with T. The current evidence does not support the belief that TTh is associated with increased CV risk or CV mortality. On the contrary, a wealth of evidence accumulated over several decades suggests that low serum T levels are associated with increased risk and that higher endogenous T, as well as TTh itself, appear to be beneficial for CV mortality and risk. PMID:25432501

  16. Succinate dehydrogenase-deficient gastrointestinal stromal tumors

    PubMed Central

    Wang, Ya-Mei; Gu, Meng-Li; Ji, Feng

    2015-01-01

    Most gastrointestinal stromal tumors (GISTs) are characterized by KIT or platelet-derived growth factor alpha (PDGFRA) activating mutations. However, there are still 10%-15% of GISTs lacking KIT and PDGFRA mutations, called wild-type GISTs (WT GISTs). Among these so-called WT GISTs, a small subset is associated with succinate dehydrogenase (SDH) deficiency, known as SDH-deficient GISTs. In addition, GISTs that occur in Carney triad and Carney-Stratakis syndrome represent specific examples of SDH-deficient GISTs. SDH-deficient GISTs locate exclusively in the stomach, showing predilection for children and young adults with female preponderance. The tumor generally pursues an indolent course and exhibits primary resistance to imatinib therapy in most cases. Loss of succinate dehydrogenase subunit B expression and overexpression of insulin-like growth factor 1 receptor (IGF1R) are common features of SDH-deficient GISTs. In WT GISTs without succinate dehydrogenase activity, upregulation of hypoxia-inducible factor 1α may lead to increased growth signaling through IGF1R and vascular endothelial growth factor receptor (VEGFR). As a result, IGF1R and VEGFR are promising to be the novel therapeutic targets of GISTs. This review will update the current knowledge on characteristics of SDH-deficient GISTs and further discuss the possible mechanisms of tumorigenesis and clinical management of SDH-deficient GISTs. PMID:25741136

  17. Fetal polyol metabolism in copper deficiency

    SciTech Connect

    Fields, M.; Lewis, C.G.; Beal, T. )

    1989-02-09

    Since pregnant rats consuming fructose, copper deficient diets fail to give birth, the relationship between maternal copper deficiency, polyol metabolism and fetal mortality was investigated. Forty Sprague-Dawley rats were fed from conception one of the following diets: fructose, copper deficient; fructose, copper adequate; starch, copper deficient or starch, copper adequate. The deficient diets contained 0.6 ug Cu and the adequate 6.0 ug Cu/g diet. Pregnancy was terminated at day 19 of gestation. Glucose, sorbitol and fructose were measured in maternal blood, placenta and fetal liver. Fructose consumption during pregnancy resulted in higher levels of fructose and sorbitol in maternal blood when compared to starch. In the fructose dietary groups, the placenta and fetal liver contained extremely high levels of glucose, fructose and sorbitol compared to the corresponding metabolites from the starch dietary groups. Copper deficiency further elevated fructose and sorbitol concentrations in the placenta and fetal liver respectively. Since high tissue levels of glucose, fructose and sorbitol have been shown to have deleterious effects on cellular metabolism, these data suggest that when fructose was fed during pregnancy the combination of an aberration of carbohydrate metabolism with copper deficiency could be responsible for the pathology and mortality of the developing fetus.

  18. Zinc: physiology, deficiency, and parenteral nutrition.

    PubMed

    Livingstone, Callum

    2015-06-01

    The essential trace element zinc (Zn) has a large number of physiologic roles, in particular being required for growth and functioning of the immune system. Adaptive mechanisms enable the body to maintain normal total body Zn status over a wide range of intakes, but deficiency can occur because of reduced absorption or increased gastrointestinal losses. Deficiency impairs physiologic processes, leading to clinical consequences that include failure to thrive, skin rash, and impaired wound healing. Mild deficiency that is not clinically overt may still cause nonspecific consequences, such as susceptibility to infection and poor growth. The plasma Zn concentration has poor sensitivity and specificity as a test of deficiency. Consequently, diagnosis of deficiency requires a combination of clinical assessment and biochemical tests. Patients receiving parenteral nutrition (PN) are susceptible to Zn deficiency and its consequences. Nutrition support teams should have a strategy for assessing Zn status and optimizing this by appropriate supplementation. Nutrition guidelines recommend generous Zn provision from the start of PN. This review covers the physiology of Zn, the consequences of its deficiency, and the assessment of its status, before discussing its role in PN. PMID:25681484

  19. Deontic Introduction: A Theory of Inference from Is to Ought

    ERIC Educational Resources Information Center

    Elqayam, Shira; Thompson, Valerie A.; Wilkinson, Meredith R.; Evans, Jonathan St. B. T.; Over, David E.

    2015-01-01

    Humans have a unique ability to generate novel norms. Faced with the knowledge that there are hungry children in Somalia, we easily and naturally infer that we ought to donate to famine relief charities. Although a contentious and lively issue in metaethics, such inference from "is" to "ought" has not been systematically…

  20. Contemporary Quantitative Methods and "Slow" Causal Inference: Response to Palinkas

    ERIC Educational Resources Information Center

    Stone, Susan

    2014-01-01

    This response considers together simultaneously occurring discussions about causal inference in social work and allied health and social science disciplines. It places emphasis on scholarship that integrates the potential outcomes model with directed acyclic graphing techniques to extract core steps in causal inference. Although this scholarship…

  1. Aging and Predicting Inferences: A Diffusion Model Analysis

    ERIC Educational Resources Information Center

    McKoon, Gail; Ratcliff, Roger

    2013-01-01

    In the domain of discourse processing, it has been claimed that older adults (60-0-year-olds) are less likely to encode and remember some kinds of information from texts than young adults. The experiment described here shows that they do make a particular kind of inference to the same extent that college-age adults do. The inferences examined were…

  2. Reasoning about Causal Relationships: Inferences on Causal Networks

    PubMed Central

    Rottman, Benjamin Margolin; Hastie, Reid

    2013-01-01

    Over the last decade, a normative framework for making causal inferences, Bayesian Probabilistic Causal Networks, has come to dominate psychological studies of inference based on causal relationships. The following causal networks—[X→Y→Z, X←Y→Z, X→Y←Z]—supply answers for questions like, “Suppose both X and Y occur, what is the probability Z occurs?” or “Suppose you intervene and make Y occur, what is the probability Z occurs?” In this review, we provide a tutorial for how normatively to calculate these inferences. Then, we systematically detail the results of behavioral studies comparing human qualitative and quantitative judgments to the normative calculations for many network structures and for several types of inferences on those networks. Overall, when the normative calculations imply that an inference should increase, judgments usually go up; when calculations imply a decrease, judgments usually go down. However, two systematic deviations appear. First, people’s inferences violate the Markov assumption. For example, when inferring Z from the structure X→Y→Z, people think that X is relevant even when Y completely mediates the relationship between X and Z. Second, even when people’s inferences are directionally consistent with the normative calculations, they are often not as sensitive to the parameters and the structure of the network as they should be. We conclude with a discussion of productive directions for future research. PMID:23544658

  3. Fostering Inference Generation with Emergent and Novice Readers

    ERIC Educational Resources Information Center

    Dougherty Stahl, Katherine A.

    2014-01-01

    Inference generation makes a strong, unique contribution to reading comprehension. Young children engage in many of the same inference generation processes as sophisticated readers. This article discusses instructional practices that can be used in prekindergarten through grade two to help children think beyond the words of the text. Suggestions…

  4. The Effect of Gender on the Construction of Backward Inferences

    ERIC Educational Resources Information Center

    Cakir, Ozler

    2008-01-01

    The main objective in the present study is to examine the effect of gender on primary school students' construction of elaborative backward inferences during text processing. A total of 333 children, aged 10-11 years (n = 158 girls and 175 boys) participated in the study. Each participant completed a backward inference test. The results indicate…

  5. Criterion Validity for Ellis' Irrational Beliefs: Dogmatism and Uncritical Inferences.

    ERIC Educational Resources Information Center

    Tobacyk, Jerome; Milford, Gary

    1982-01-01

    Tested a sample of college students to determine the validity of Ellis' contention that irrational beliefs: (1) are held dogmatically and (2) interfere with logical inference making. Found greater endorsement of irrational beliefs on the Irrational Belief Scale associated with (1) greater dogmatism and (2) less critical inference making.…

  6. The Strong-Inference Protocol: Not Just for Grant Proposals

    ERIC Educational Resources Information Center

    Hiebert, Sara M.

    2007-01-01

    The strong-inference protocol puts into action the important concepts in Platt's often-assigned, classic paper on the strong-inference method (10). Yet, perhaps because students are frequently performing experiments with known outcomes, the protocols they write as undergraduates are usually little more than step-by-step instructions for performing…

  7. Developing Young Students' Informal Inference Skills in Data Analysis

    ERIC Educational Resources Information Center

    Paparistodemou, Efi; Meletiou-Mavrotheris, Maria

    2008-01-01

    This paper focuses on developing students' informal inference skills, reporting on how a group of third grade students formulated and evaluated data-based inferences using the dynamic statistics data-visualization environment TinkerPlots[TM] (Konold & Miller, 2005), software specifically designed to meet the learning needs of students in the early…

  8. Strategic Processing and Predictive Inference Generation in L2 Reading

    ERIC Educational Resources Information Center

    Nahatame, Shingo

    2014-01-01

    Predictive inference is the anticipation of the likely consequences of events described in a text. This study investigated predictive inference generation during second language (L2) reading, with a focus on the effects of strategy instructions. In this experiment, Japanese university students read several short narrative passages designed to…

  9. Another Look At The Canon of Plausible Inference

    NASA Astrophysics Data System (ADS)

    Solana-Ortega, Alberto; Solana, Vicente

    2005-11-01

    Systematic study of plausible inference is very recent. Axiomatics have been traditionally limited to the development of uninterpreted pure calculi for comparing individual inferences, ignoring the need of formalisms to solve each of these inferences and leaving the interpretation and application of such calculi to ad hoc statistical criteria which are open to inconsistencies. Here we defend a different viewpoint, regarding plausible inference in a holistic manner. Specifically we consider that all tasks involved in it, including the formalization of languages in which to pose problems, the definitions and axiomatics leading to calculation rules and those for deriving inference procedures or assignment rules, ought to be based on common grounds. For this purpose a set of elementary requirements establishing desirable properties so fundamental any theory of scientific inference should satisfy is proposed under the name of plausible inference canon. Its logical status as an extramathematical foundation is investigated, together with the different roles it plays as constructive guideline, standard for contrasting frameworks or normative stipulation. We also highlight the novelties it introduces with respect to similar proposals by other authors. In particular we concentrate on those aspects of the canon related to the critical issue of adequately incorporating basic evidential knowledge to inference.

  10. Exploring Beginning Inference with Novice Grade 7 Students

    ERIC Educational Resources Information Center

    Watson, Jane M.

    2008-01-01

    This study documented efforts to facilitate ideas of beginning inference in novice grade 7 students. A design experiment allowed modified teaching opportunities in light of observation of components of a framework adapted from that developed by Pfannkuch for teaching informal inference with box plots. Box plots were replaced by hat plots, a…

  11. Inferencing Processes after Right Hemisphere Brain Damage: Maintenance of Inferences

    ERIC Educational Resources Information Center

    Blake, Margaret Lehman

    2009-01-01

    Purpose: This study was designed to replicate and extend a previous study of inferencing in which some adults with right hemisphere damage (RHD) generated but did not maintain predictive inferences over time (M. Lehman-Blake & C. Tompkins, 2001). Two hypotheses were tested: (a) inferences were deactivated, and (b) selection of previously generated…

  12. A Probability Index of the Robustness of a Causal Inference

    ERIC Educational Resources Information Center

    Pan, Wei; Frank, Kenneth A.

    2003-01-01

    Causal inference is an important, controversial topic in the social sciences, where it is difficult to conduct experiments or measure and control for all confounding variables. To address this concern, the present study presents a probability index to assess the robustness of a causal inference to the impact of a confounding variable. The…

  13. Causal inference with a quantitative exposure.

    PubMed

    Zhang, Zhiwei; Zhou, Jie; Cao, Weihua; Zhang, Jun

    2016-02-01

    The current statistical literature on causal inference is mostly concerned with binary or categorical exposures, even though exposures of a quantitative nature are frequently encountered in epidemiologic research. In this article, we review the available methods for estimating the dose-response curve for a quantitative exposure, which include ordinary regression based on an outcome regression model, inverse propensity weighting and stratification based on a propensity function model, and an augmented inverse propensity weighting method that is doubly robust with respect to the two models. We note that an outcome regression model often imposes an implicit constraint on the dose-response curve, and propose a flexible modeling strategy that avoids constraining the dose-response curve. We also propose two new methods: a weighted regression method that combines ordinary regression with inverse propensity weighting and a stratified regression method that combines ordinary regression with stratification. The proposed methods are similar to the augmented inverse propensity weighting method in the sense of double robustness, but easier to implement and more generally applicable. The methods are illustrated with an obstetric example and compared in simulation studies. PMID:22729475

  14. Relationship inference based on DNA mixtures.

    PubMed

    Kaur, Navreet; Bouzga, Mariam M; Dørum, Guro; Egeland, Thore

    2016-03-01

    Today, there exists a number of tools for solving kinship cases. But what happens when information comes from a mixture? DNA mixtures are in general rarely seen in kinship cases, but in a case presented to the Norwegian Institute of Public Health, sample DNA was obtained after a rape case that resulted in an unwanted pregnancy and abortion. The only available DNA from the fetus came in form of a mixture with the mother, and it was of interest to find the father of the fetus. The mother (the victim), however, refused to give her reference data and so commonly used methods for paternity testing were no longer applicable. As this case illustrates, kinship cases involving mixtures and missing reference profiles do occur and make the use of existing methods rather inconvenient. We here present statistical methods that may handle general relationship inference based on DNA mixtures. The basic idea is that likelihood calculations for mixtures can be decomposed into a series of kinship problems. This formulation of the problem facilitates the use of kinship software. We present the freely available R package relMix which extends on the R version of Familias. Complicating factors like mutations, silent alleles, and θ-correction are then easily handled for quite general family relationships, and are included in the statistical methods we develop in this paper. The methods and their implementations are exemplified on the data from the rape case. PMID:26541994

  15. Aesthetic quality inference for online fashion shopping

    NASA Astrophysics Data System (ADS)

    Chen, Ming; Allebach, Jan

    2014-03-01

    On-line fashion communities in which participants post photos of personal fashion items for viewing and possible purchase by others are becoming increasingly popular. Generally, these photos are taken by individuals who have no training in photography with low-cost mobile phone cameras. It is desired that photos of the products have high aesthetic quality to improve the users' online shopping experience. In this work, we design features for aesthetic quality inference in the context of online fashion shopping. Psychophysical experiments are conducted to construct a database of the photos' aesthetic evaluation, specifically for photos from an online fashion shopping website. We then extract both generic low-level features and high-level image attributes to represent the aesthetic quality. Using a support vector machine framework, we train a predictor of the aesthetic quality rating based on the feature vector. Experimental results validate the efficacy of our approach. Metadata such as the product type are also used to further improve the result.

  16. Robust sharp features infer from point clouds

    NASA Astrophysics Data System (ADS)

    Cao, Juming; Wushour, Slam; Yao, Xinhui; Li, NaiQian; Liang, Jin; Liang, Xinhe; Liu, Jianwei

    2011-07-01

    A novel sharp features extraction method is proposed in this paper. First, we calculate the displacement between the point and its local weighted average position and we label the point with salient this value as the candidate sharp feature points and we estimate the normal direction of those candidate sharp feature points by means of local PCA methods. Then we refine the normal estimated by inferring the orientation of the points near the candidate sharp feature region and bilateral filtering in the normal field of point clouds. At last we project the displacement between point and its local weighted average position along the direction of normal .We use value of this projection as the criteria of whether a point can be labeled as sharp feature. The extracted discrete sharp feature points are represented in the form of piecewised B-Spline lines. Experiment on both real scanner point clouds and synthesized point clouds show that our method of sharp features extraction are simple to be implemented and efficient for both space and time overhead as well as it robust to the noise ,outlier and un even sample witch are inherent in the point clouds.

  17. Active Inference and Learning in the Cerebellum.

    PubMed

    Friston, Karl; Herreros, Ivan

    2016-09-01

    This letter offers a computational account of Pavlovian conditioning in the cerebellum based on active inference and predictive coding. Using eyeblink conditioning as a canonical paradigm, we formulate a minimal generative model that can account for spontaneous blinking, startle responses, and (delay or trace) conditioning. We then establish the face validity of the model using simulated responses to unconditioned and conditioned stimuli to reproduce the sorts of behavior that are observed empirically. The scheme's anatomical validity is then addressed by associating variables in the predictive coding scheme with nuclei and neuronal populations to match the (extrinsic and intrinsic) connectivity of the cerebellar (eyeblink conditioning) system. Finally, we try to establish predictive validity by reproducing selective failures of delay conditioning, trace conditioning, and extinction using (simulated and reversible) focal lesions. Although rather metaphorical, the ensuing scheme can account for a remarkable range of anatomical and neurophysiological aspects of cerebellar circuitry-and the specificity of lesion-deficit mappings that have been established experimentally. From a computational perspective, this work shows how conditioning or learning can be formulated in terms of minimizing variational free energy (or maximizing Bayesian model evidence) using exactly the same principles that underlie predictive coding in perception. PMID:27391681

  18. Attention as a Bayesian inference process

    NASA Astrophysics Data System (ADS)

    Chikkerur, Sharat; Serre, Thomas; Tan, Cheston; Poggio, Tomaso

    2011-03-01

    David Marr famously defined vision as "knowing what is where by seeing". In the framework described here, attention is the inference process that solves the visual recognition problem of what is where. The theory proposes a computational role for attention and leads to a model that performs well in recognition tasks and that predicts some of the main properties of attention at the level of psychophysics and physiology. We propose an algorithmic implementation a Bayesian network that can be mapped into the basic functional anatomy of attention involving the ventral stream and the dorsal stream. This description integrates bottom-up, feature-based as well as spatial (context based) attentional mechanisms. We show that the Bayesian model predicts well human eye fixations (considered as a proxy for shifts of attention) in natural scenes, and can improve accuracy in object recognition tasks involving cluttered real world images. In both cases, we found that the proposed model can predict human performance better than existing bottom-up and top-down computational models.

  19. Noise Sensitivity in Force-inference Techniques

    NASA Astrophysics Data System (ADS)

    Mashburn, David N.; Hutson, M. Shane; Veldhuis, Jim H.; Brodland, G. Wayne

    2014-03-01

    Forward finite-element modeling of developmental processes has vastly improved our understanding of morphogenesis; however, determining the model parameters necessary to reproduce in vivo behaviors typically requires either computationally-intensive parameter searches or somewhat arbitrary user selections. To bypass these difficulties, we previously developed an inverse technique called Video Force Microscopy (VFM) that takes positional information from microscopy data and infers the forces necessary to reproduce the observed dynamics. Applying VFM to the output of a forward model produces exact results, but the over-determined solutions for any real data will generally have a nonzero residual error. Applying VFM to real images requires converting the image into a segmented mesh of polygonal cells, a process in which the image resolution creates inherent positional noise and the choice of mesh nodes influences the angles used in the force balance equations. We have investigated the robustness and quality of VFM solutions by analyzing sensitivity to both the unavoidable positional noise and addition/removal of mesh nodes. We have also evaluated the accuracy of both the residual and the matrix condition numbers as predictors of the true error (as measured against a gold standard).

  20. The renormalization group via statistical inference

    NASA Astrophysics Data System (ADS)

    Bény, Cédric; Osborne, Tobias J.

    2015-08-01

    In physics, one attempts to infer the rules governing a system given only the results of imperfect measurements. Hence, microscopic theories may be effectively indistinguishable experimentally. We develop an operationally motivated procedure to identify the corresponding equivalence classes of states, and argue that the renormalization group (RG) arises from the inherent ambiguities associated with the classes: one encounters flow parameters as, e.g., a regulator, a scale, or a measure of precision, which specify representatives in a given equivalence class. This provides a unifying framework and reveals the role played by information in renormalization. We validate this idea by showing that it justifies the use of low-momenta n-point functions as statistically relevant observables around a Gaussian hypothesis. These results enable the calculation of distinguishability in quantum field theory. Our methods also provide a way to extend renormalization techniques to effective models which are not based on the usual quantum-field formalism, and elucidates the relationships between various type of RG.

  1. Inference evaluation in a finite evidence domain

    NASA Astrophysics Data System (ADS)

    Ratway, Michael J.; Bellomo, Carryn

    2000-08-01

    Modeling of a target starts with a subject matter expert (SME) analysis of the available sensor(s) data. The SME then forms relationships between the data and known target attributes, called evidence, to support modeling of different types of targets or target activity. Speeds in the interval 10 to 30 knots and ranges less than 30 nautical miles are two samples of target evidence derived from sensor data. Evidence is then organized into sets to define the activities of a target and/or to distinguish different types of targets. For example, near an airport, target activities of takeoff, landing, and holding need to be evaluated in addition to target classification of civilian or commercial aircraft. This paper discusses a method for evaluation of the inferred activities over the finite evidence domain formed from the collection of models under consideration. The methodology accounts for repeated use of evidence in different models. For example, 'near an airport' is a required piece of evidence used repeatedly in the takeoff, landing, and holding models of a wide area sensor. Properties of the activity model evaluator methodology are discussed in terms of model construction and informal results are presented in a Boolean evidence type of problem domain.

  2. Impact of nonignorable coarsening on Bayesian inference.

    PubMed

    Zhang, Jiameng; Heitjan, Daniel F

    2007-10-01

    The coarse data model of Heitjan and Rubin (1991) generalizes the missing data model of Rubin (1976) to cover other forms of incompleteness such as censoring and grouping. The model has 2 components: an ideal data model describing the distribution of the quantity of interest and a coarsening mechanism that describes a distribution over degrees of coarsening given the ideal data. The coarsening mechanism is said to be nonignorable when the degree of coarsening depends on an incompletely observed ideal outcome, in which case failure to properly account for it can spoil inferences. A theme in recent research is to measure sensitivity to nonignorability by evaluating the effect of a small departure from ignorability on the maximum likelihood estimate (MLE) of a parameter of the ideal data model. One such construct is the "index of local sensitivity to nonignorability" (ISNI) (Troxel and others, 2004), which is the derivative of the MLE with respect to a nonignorability parameter evaluated at the ignorable model. In this paper, we adapt ISNI to Bayesian modeling by instead defining it as the derivative of the posterior expectation. We propose the application of ISNI as a first step in judging the robustness of a Bayesian analysis to nonignorable coarsening. We derive formulas for a range of models and apply the method to evaluate sensitivity to nonignorable coarsening in 2 real data examples, one involving missing CD4 counts in an HIV trial and the other involving potentially informatively censored relapse times in a leukemia trial. PMID:17215331

  3. Inferring human mobility using communication patterns

    NASA Astrophysics Data System (ADS)

    Palchykov, Vasyl; Mitrović, Marija; Jo, Hang-Hyun; Saramäki, Jari; Pan, Raj Kumar

    2014-08-01

    Understanding the patterns of mobility of individuals is crucial for a number of reasons, from city planning to disaster management. There are two common ways of quantifying the amount of travel between locations: by direct observations that often involve privacy issues, e.g., tracking mobile phone locations, or by estimations from models. Typically, such models build on accurate knowledge of the population size at each location. However, when this information is not readily available, their applicability is rather limited. As mobile phones are ubiquitous, our aim is to investigate if mobility patterns can be inferred from aggregated mobile phone call data alone. Using data released by Orange for Ivory Coast, we show that human mobility is well predicted by a simple model based on the frequency of mobile phone calls between two locations and their geographical distance. We argue that the strength of the model comes from directly incorporating the social dimension of mobility. Furthermore, as only aggregated call data is required, the model helps to avoid potential privacy problems.

  4. Atomic Inference from Weak Gravitational Lensing Data

    SciTech Connect

    Marshall, Phil; /KIPAC, Menlo Park

    2005-12-14

    We present a novel approach to reconstructing the projected mass distribution from the sparse and noisy weak gravitational lensing shear data. The reconstructions are regularized via the knowledge gained from numerical simulations of clusters, with trial mass distributions constructed from n NFW profile ellipsoidal components. The parameters of these ''atoms'' are distributed a priori as in the simulated clusters. Sampling the mass distributions from the atom parameter probability density function allows estimates of the properties of the mass distribution to be generated, with error bars. The appropriate number of atoms is inferred from the data itself via the Bayesian evidence, and is typically found to be small, reecting the quality of the data. Ensemble average mass maps are found to be robust to the details of the noise realization, and succeed in recovering the demonstration input mass distribution (from a realistic simulated cluster) over a wide range of scales. As an application of such a reliable mapping algorithm, we comment on the residuals of the reconstruction and the implications for predicting convergence and shear at specific points on the sky.

  5. Probabilistic phylogenetic inference with insertions and deletions.

    PubMed

    Rivas, Elena; Eddy, Sean R

    2008-01-01

    A fundamental task in sequence analysis is to calculate the probability of a multiple alignment given a phylogenetic tree relating the sequences and an evolutionary model describing how sequences change over time. However, the most widely used phylogenetic models only account for residue substitution events. We describe a probabilistic model of a multiple sequence alignment that accounts for insertion and deletion events in addition to substitutions, given a phylogenetic tree, using a rate matrix augmented by the gap character. Starting from a continuous Markov process, we construct a non-reversible generative (birth-death) evolutionary model for insertions and deletions. The model assumes that insertion and deletion events occur one residue at a time. We apply this model to phylogenetic tree inference by extending the program dnaml in phylip. Using standard benchmarking methods on simulated data and a new "concordance test" benchmark on real ribosomal RNA alignments, we show that the extended program dnamlepsilon improves accuracy relative to the usual approach of ignoring gaps, while retaining the computational efficiency of the Felsenstein peeling algorithm. PMID:18787703

  6. Inference by replication in densely connected systems.

    PubMed

    Neirotti, Juan P; Saad, David

    2007-10-01

    An efficient Bayesian inference method for problems that can be mapped onto dense graphs is presented. The approach is based on message passing where messages are averaged over a large number of replicated variable systems exposed to the same evidential nodes. An assumption about the symmetry of the solutions is required for carrying out the averages; here we extend the previous derivation based on a replica-symmetric- (RS)-like structure to include a more complex one-step replica-symmetry-breaking-like (1RSB-like) ansatz. To demonstrate the potential of the approach it is employed for studying critical properties of the Ising linear perceptron and for multiuser detection in code division multiple access (CDMA) under different noise models. Results obtained under the RS assumption in the noncritical regime give rise to a highly efficient signal detection algorithm in the context of CDMA; while in the critical regime one observes a first-order transition line that ends in a continuous phase transition point. Finite size effects are also observed. While the 1RSB ansatz is not required for the original problems, it was applied to the CDMA signal detection problem with a more complex noise model that exhibits RSB behavior, resulting in an improvement in performance. PMID:17995074

  7. Bayesian Inference of CMB Gravitational Lensing

    NASA Astrophysics Data System (ADS)

    Anderes, Ethan; Wandelt, Benjamin D.; Lavaux, Guilhem

    2015-08-01

    The Planck satellite, along with several ground-based telescopes, has mapped the cosmic microwave background (CMB) at sufficient resolution and signal-to-noise so as to allow a detection of the subtle distortions due to the gravitational influence of the intervening matter distribution. A natural modeling approach is to write a Bayesian hierarchical model for the lensed CMB in terms of the unlensed CMB and the lensing potential. So far there has been no feasible algorithm for inferring the posterior distribution of the lensing potential from the lensed CMB map. We propose a solution that allows efficient Markov Chain Monte Carlo sampling from the joint posterior of the lensing potential and the unlensed CMB map using the Hamiltonian Monte Carlo technique. The main conceptual step in the solution is a re-parameterization of CMB lensing in terms of the lensed CMB and the “inverse lensing” potential. We demonstrate a fast implementation on simulated data, including noise and a sky cut, that uses a further acceleration based on a very mild approximation of the inverse lensing potential. We find that the resulting Markov Chain has short correlation lengths and excellent convergence properties, making it promising for applications to high-resolution CMB data sets in the future.

  8. Virtual reality and consciousness inference in dreaming.

    PubMed

    Hobson, J Allan; Hong, Charles C-H; Friston, Karl J

    2014-01-01

    This article explores the notion that the brain is genetically endowed with an innate virtual reality generator that - through experience-dependent plasticity - becomes a generative or predictive model of the world. This model, which is most clearly revealed in rapid eye movement (REM) sleep dreaming, may provide the theater for conscious experience. Functional neuroimaging evidence for brain activations that are time-locked to rapid eye movements (REMs) endorses the view that waking consciousness emerges from REM sleep - and dreaming lays the foundations for waking perception. In this view, the brain is equipped with a virtual model of the world that generates predictions of its sensations. This model is continually updated and entrained by sensory prediction errors in wakefulness to ensure veridical perception, but not in dreaming. In contrast, dreaming plays an essential role in maintaining and enhancing the capacity to model the world by minimizing model complexity and thereby maximizing both statistical and thermodynamic efficiency. This perspective suggests that consciousness corresponds to the embodied process of inference, realized through the generation of virtual realities (in both sleep and wakefulness). In short, our premise or hypothesis is that the waking brain engages with the world to predict the causes of sensations, while in sleep the brain's generative model is actively refined so that it generates more efficient predictions during waking. We review the evidence in support of this hypothesis - evidence that grounds consciousness in biophysical computations whose neuronal and neurochemical infrastructure has been disclosed by sleep research. PMID:25346710

  9. Bell's theorem, inference, and quantum transactions

    NASA Astrophysics Data System (ADS)

    Garrett, A. J. M.

    1990-04-01

    Bell's theorem is expounded as an analysis in Bayesian inference. Assuming the result of a spin measurement on a particle is governed by a causal variable internal (hidden, “local”) to the particle, one learns about it by making a spin measurement; thence about the internal variable of a second particle correlated with the first; and from there predicts the probabilistic result of spin measurements on the second particle. Such predictions are violated by experiment: locality/causality fails. The statistical nature of the observations rules out signalling; acausal, superluminal, or otherwise. Quantum mechanics is irrelevant to this reasoning, although its correct predictions of experiment imply that it has a nonlocal/acausal interpretation. Cramer's new transactional interpretation, which incorporates this feature by adapting the Wheeler-Feynman idea of advanced and retarded processes to the quantum laws, is advocated. It leads to an invaluable way of envisaging quantum processes. The usual paradoxes melt before this, and one, the “delayed choice” experiment, is chosen for detailed inspection. Nonlocality implies practical difficulties in influencing hidden variables, which provides a very plausible explanation for why they have not yet been found; from this standpoint, Bell's theorem reinforces arguments in favor of hidden variables.

  10. Functional network inference of the suprachiasmatic nucleus.

    PubMed

    Abel, John H; Meeker, Kirsten; Granados-Fuentes, Daniel; St John, Peter C; Wang, Thomas J; Bales, Benjamin B; Doyle, Francis J; Herzog, Erik D; Petzold, Linda R

    2016-04-19

    In the mammalian suprachiasmatic nucleus (SCN), noisy cellular oscillators communicate within a neuronal network to generate precise system-wide circadian rhythms. Although the intracellular genetic oscillator and intercellular biochemical coupling mechanisms have been examined previously, the network topology driving synchronization of the SCN has not been elucidated. This network has been particularly challenging to probe, due to its oscillatory components and slow coupling timescale. In this work, we investigated the SCN network at a single-cell resolution through a chemically induced desynchronization. We then inferred functional connections in the SCN by applying the maximal information coefficient statistic to bioluminescence reporter data from individual neurons while they resynchronized their circadian cycling. Our results demonstrate that the functional network of circadian cells associated with resynchronization has small-world characteristics, with a node degree distribution that is exponential. We show that hubs of this small-world network are preferentially located in the central SCN, with sparsely connected shells surrounding these cores. Finally, we used two computational models of circadian neurons to validate our predictions of network structure. PMID:27044085

  11. Inference by replication in densely connected systems

    SciTech Connect

    Neirotti, Juan P.; Saad, David

    2007-10-15

    An efficient Bayesian inference method for problems that can be mapped onto dense graphs is presented. The approach is based on message passing where messages are averaged over a large number of replicated variable systems exposed to the same evidential nodes. An assumption about the symmetry of the solutions is required for carrying out the averages; here we extend the previous derivation based on a replica-symmetric- (RS)-like structure to include a more complex one-step replica-symmetry-breaking-like (1RSB-like) ansatz. To demonstrate the potential of the approach it is employed for studying critical properties of the Ising linear perceptron and for multiuser detection in code division multiple access (CDMA) under different noise models. Results obtained under the RS assumption in the noncritical regime give rise to a highly efficient signal detection algorithm in the context of CDMA; while in the critical regime one observes a first-order transition line that ends in a continuous phase transition point. Finite size effects are also observed. While the 1RSB ansatz is not required for the original problems, it was applied to the CDMA signal detection problem with a more complex noise model that exhibits RSB behavior, resulting in an improvement in performance.

  12. Virtual reality and consciousness inference in dreaming

    PubMed Central

    Hobson, J. Allan; Hong, Charles C.-H.; Friston, Karl J.

    2014-01-01

    This article explores the notion that the brain is genetically endowed with an innate virtual reality generator that – through experience-dependent plasticity – becomes a generative or predictive model of the world. This model, which is most clearly revealed in rapid eye movement (REM) sleep dreaming, may provide the theater for conscious experience. Functional neuroimaging evidence for brain activations that are time-locked to rapid eye movements (REMs) endorses the view that waking consciousness emerges from REM sleep – and dreaming lays the foundations for waking perception. In this view, the brain is equipped with a virtual model of the world that generates predictions of its sensations. This model is continually updated and entrained by sensory prediction errors in wakefulness to ensure veridical perception, but not in dreaming. In contrast, dreaming plays an essential role in maintaining and enhancing the capacity to model the world by minimizing model complexity and thereby maximizing both statistical and thermodynamic efficiency. This perspective suggests that consciousness corresponds to the embodied process of inference, realized through the generation of virtual realities (in both sleep and wakefulness). In short, our premise or hypothesis is that the waking brain engages with the world to predict the causes of sensations, while in sleep the brain’s generative model is actively refined so that it generates more efficient predictions during waking. We review the evidence in support of this hypothesis – evidence that grounds consciousness in biophysical computations whose neuronal and neurochemical infrastructure has been disclosed by sleep research. PMID:25346710

  13. Severe Vitamin D Deficiency Causing Kyphoscoliosis.

    PubMed

    Singhai, Abhishek; Banzal, Subodh

    2013-01-01

    Vitamin D deficiency is common among Indian population. Women are especially at risk for severe vitamin D deficiency. The risk is higher for those who are multiparous and postmenopausal. Poor exposure to sunlight, higher latitude, winter season, inadequate diet, older age, obesity and malabsorption are also important risk factors. Symptoms of hypovitaminosis D, including diffuse or migratory pain affecting several sites (especially the shoulder, pelvis, ribcage and lower back) have also been misdiagnosed as musculoskeletal disorders, including fibromyalgia, polymyalgia rheumatica and ankylosing spondylitis. Here, we report two cases presented with kyphoscoliosis, diagnosed to have severe vitamin D deficiency. PMID:26664847

  14. Auditory Neuropathy/Dyssynchrony in Biotinidase Deficiency

    PubMed Central

    Yaghini, Omid

    2016-01-01

    Biotinidase deficiency is a disorder inherited autosomal recessively showing evidence of hearing loss and optic atrophy in addition to seizures, hypotonia, and ataxia. In the present study, a 2-year-old boy with Biotinidase deficiency is presented in which clinical symptoms have been reported with auditory neuropathy/auditory dyssynchrony (AN/AD). In this case, transient-evoked otoacoustic emissions showed bilaterally normal responses representing normal function of outer hair cells. In contrast, acoustic reflex test showed absent reflexes bilaterally, and visual reinforcement audiometry and auditory brainstem responses indicated severe to profound hearing loss in both ears. These results suggest AN/AD in patients with Biotinidase deficiency. PMID:27144235

  15. Severe Vitamin D Deficiency Causing Kyphoscoliosis

    PubMed Central

    Singhai, Abhishek; Banzal, Subodh

    2013-01-01

    Vitamin D deficiency is common among Indian population. Women are especially at risk for severe vitamin D deficiency. The risk is higher for those who are multiparous and postmenopausal. Poor exposure to sunlight, higher latitude, winter season, inadequate diet, older age, obesity and malabsorption are also important risk factors. Symptoms of hypovitaminosis D, including diffuse or migratory pain affecting several sites (especially the shoulder, pelvis, ribcage and lower back) have also been misdiagnosed as musculoskeletal disorders, including fibromyalgia, polymyalgia rheumatica and ankylosing spondylitis. Here, we report two cases presented with kyphoscoliosis, diagnosed to have severe vitamin D deficiency. PMID:26664847

  16. Unilateral Isolated Proximal Femoral Focal Deficiency

    PubMed Central

    Doğer, Emek; Köpük, Şule Y.; Çakıroğlu, Yiğit; Çakır, Özgür; Yücesoy, Gülseren

    2013-01-01

    Objective. To discuss a patient with a prenatal diagnosis of unilateral isolated femoral focal deficiency. Case. Antenatal diagnosis of unilateral isolated femoral focal deficiency was made at 20 weeks of gestation. The length of left femur was shorter than the right, and fetal femur length was below the fifth percentile. Proximal femoral focal deficiency was diagnosed. After delivery, the diagnosis was confirmed with skeletal radiographs and magnetic resonance imaging. In prenatal ultrasonographic examination, the early recognition and exclusion of skeletal dysplasias is important; moreover, treatment plans should be initiated, and valuable information should be provided to the family. PMID:23984135

  17. Factor X deficiency in a cat.

    PubMed

    Gookin, J L; Brooks, M B; Catalfamo, J L; Bunch, S E; Muñana, K R

    1997-09-01

    Severe congenital deficiency of factor X was diagnosed in a 3-year-old castrated male domestic shorthair cat with clinical signs of generalized seizures and prolonged bleeding after venipuncture. Heritability of factor X deficiency was suspected because of a prolonged Russell's viper venom time in the dam and reductions in factor X activity in the dam and 1 sibling. To our knowledge, factor X deficiency in cats has not been reported previously. Definitive diagnosis for animals with clinical signs of coagulopathy may require repetition of coagulation screening tests using different assay methods or specific coagulation factor analyses. PMID:9290823

  18. Vitamin B12 deficiency: the great masquerader.

    PubMed

    Dobrozsi, Sarah; Flood, Veronica H; Panepinto, Julie; Scott, J Paul; Brandow, Amanda

    2014-04-01

    Vitamin B12 deficiency is rare in children, with nonspecific symptoms including failure to thrive, vomiting, anorexia, and neurologic changes with or without hematologic disturbances. The neuropathy can be severe and irreversible. We report four cases of children with B12 deficiency secondary to adult type pernicious anemia, a presumed transport protein abnormality, and a metabolic defect. All demonstrated neurologic compromise that improved after initiation of B12 therapy. Hematologic manifestations may be preceded by constitutional, gastrointestinal, or neurologic changes, and must raise concern for B12 deficiency. Therapy should be initiated promptly in this setting to prevent irreversible neuropathy. PMID:24115632

  19. Cobalamin deficiency triggering de novo status epilepticus.

    PubMed

    Anastogiannis, Haralabos; Karanasios, Panagiotis; Makridou, Alexandra; Makris, Nicolaos; Argyriou, Andreas A

    2014-03-01

    Cobalamin deficiency is included in the spectrum of very uncommon underlying causes of status epilepticus (SE) and the literature contains very few such cases. We herein report a case of unusual presentation of cobalamin (vitamin B12) deficiency with de novo SE with the intention to bolster the argument that a de novo manifestation of SE due to cobalamin deficiency might not be that uncommon. We also support the importance of prompt identification and treatment of the underlying causes of SE, particularly those which are uncommon. PMID:24659635

  20. Nutrition and hair: deficiencies and supplements.

    PubMed

    Finner, Andreas M

    2013-01-01

    Hair follicle cells have a high turnover. A caloric deprivation or deficiency of several components, such as proteins, minerals, essential fatty acids, and vitamins, caused by inborn errors or reduced uptake, can lead to structural abnormalities, pigmentation changes, or hair loss, although exact data are often lacking. The diagnosis is established through a careful history, clinical examination of hair loss activity, and hair quality and confirmed through targeted laboratory tests. Examples of genetic hair disorders caused by reduced nutritional components are zinc deficiency in acrodermatitis enteropathica and copper deficiency in Menkes kinky hair syndrome. PMID:23159185

  1. Quantum-Like Representation of Non-Bayesian Inference

    NASA Astrophysics Data System (ADS)

    Asano, M.; Basieva, I.; Khrennikov, A.; Ohya, M.; Tanaka, Y.

    2013-01-01

    This research is related to the problem of "irrational decision making or inference" that have been discussed in cognitive psychology. There are some experimental studies, and these statistical data cannot be described by classical probability theory. The process of decision making generating these data cannot be reduced to the classical Bayesian inference. For this problem, a number of quantum-like coginitive models of decision making was proposed. Our previous work represented in a natural way the classical Bayesian inference in the frame work of quantum mechanics. By using this representation, in this paper, we try to discuss the non-Bayesian (irrational) inference that is biased by effects like the quantum interference. Further, we describe "psychological factor" disturbing "rationality" as an "environment" correlating with the "main system" of usual Bayesian inference.

  2. Identifiability and inference of pathway motifs by epistasis analysis.

    PubMed

    Phenix, Hilary; Perkins, Theodore; Kærn, Mads

    2013-06-01

    The accuracy of genetic network inference is limited by the assumptions used to determine if one hypothetical model is better than another in explaining experimental observations. Most previous work on epistasis analysis-in which one attempts to infer pathway relationships by determining equivalences among traits following mutations-has been based on Boolean or linear models. Here, we delineate the ultimate limits of epistasis-based inference by systematically surveying all two-gene network motifs and use symbolic algebra with arbitrary regulation functions to examine trait equivalences. Our analysis divides the motifs into equivalence classes, where different genetic perturbations result in indistinguishable experimental outcomes. We demonstrate that this partitioning can reveal important information about network architecture, and show, using simulated data, that it greatly improves the accuracy of genetic network inference methods. Because of the minimal assumptions involved, equivalence partitioning has broad applicability for gene network inference. PMID:23822501

  3. Wisdom of crowds for robust gene network inference

    PubMed Central

    Marbach, Daniel; Costello, James C.; Küffner, Robert; Vega, Nicci; Prill, Robert J.; Camacho, Diogo M.; Allison, Kyle R.; Kellis, Manolis; Collins, James J.; Stolovitzky, Gustavo

    2012-01-01

    Reconstructing gene regulatory networks from high-throughput data is a long-standing problem. Through the DREAM project (Dialogue on Reverse Engineering Assessment and Methods), we performed a comprehensive blind assessment of over thirty network inference methods on Escherichia coli, Staphylococcus aureus, Saccharomyces cerevisiae, and in silico microarray data. We characterize performance, data requirements, and inherent biases of different inference approaches offering guidelines for both algorithm application and development. We observe that no single inference method performs optimally across all datasets. In contrast, integration of predictions from multiple inference methods shows robust and high performance across diverse datasets. Thereby, we construct high-confidence networks for E. coli and S. aureus, each comprising ~1700 transcriptional interactions at an estimated precision of 50%. We experimentally test 53 novel interactions in E. coli, of which 23 were supported (43%). Our results establish community-based methods as a powerful and robust tool for the inference of transcriptional gene regulatory networks. PMID:22796662

  4. Identifiability and inference of pathway motifs by epistasis analysis

    NASA Astrophysics Data System (ADS)

    Phenix, Hilary; Perkins, Theodore; Kærn, Mads

    2013-06-01

    The accuracy of genetic network inference is limited by the assumptions used to determine if one hypothetical model is better than another in explaining experimental observations. Most previous work on epistasis analysis—in which one attempts to infer pathway relationships by determining equivalences among traits following mutations—has been based on Boolean or linear models. Here, we delineate the ultimate limits of epistasis-based inference by systematically surveying all two-gene network motifs and use symbolic algebra with arbitrary regulation functions to examine trait equivalences. Our analysis divides the motifs into equivalence classes, where different genetic perturbations result in indistinguishable experimental outcomes. We demonstrate that this partitioning can reveal important information about network architecture, and show, using simulated data, that it greatly improves the accuracy of genetic network inference methods. Because of the minimal assumptions involved, equivalence partitioning has broad applicability for gene network inference.

  5. Skin wound healing in MMP2-deficient and MMP2 / plasminogen double-deficient mice.

    PubMed

    Frøssing, Signe; Rønø, Birgitte; Hald, Andreas; Rømer, John; Lund, Leif R

    2010-08-01

    During healing of incisional skin wounds, migrating keratinocytes dissect their way under the crust to re-epithelialize the wounded area. The efficiency of this tissue remodelling process depends on the concomitant activity of several extracellular proteases, including members of the plasminogen activation (PA) system and the matrix metalloproteinase (MMP) family. Treatment with the broad spectrum MMP inhibitor, galardin, delays wound healing in wildtype mice and completely arrest wound healing in plasminogen (Plg)-deficient mice, indicating a functional overlap between plasmin- and galardin-sensitive MMPs during wound healing. To address whether MMP2 is accountable for the galardin-induced healing deficiency in wildtype and Plg-deficient mice, incisional skin wounds were generated in MMP2 single-deficient mice and in MMP2/Plg double-deficient mice and followed until healed. Alternatively, tissue was isolated 7 days post wounding for histological and biochemical analyses. No difference was found in the time from wounding to overt gross restoration of the epidermal surface between MMP2-deficient and wildtype control littermate mice. MMP2/Plg double-deficient mice were viable and fertile, and displayed an unchallenged general phenotype resembling that of Plg-deficient mice, including development of rectal prolapses. MMP2/Plg double-deficient mice displayed a slight increase in the wound length throughout the healing period compared with Plg-deficient mice. However, the overall time to complete healing was not significantly different between Plg-deficient and MMP2/Plg double-deficient mice. These results show that MMP2 activity is not essential for wound healing and indicate that lack of MMP2 only marginally potentiates the effect of Plg deficiency. PMID:20163454

  6. [Clinical, biological and genetic heterogeneity of the inborn errors of pulmonary surfactant metabolism: SP-B deficiency and alveolar proteinosis].

    PubMed

    Tredano, M; Blic, J D; Griese, M; Fournet, J C; Elion, J; Bahuau, M

    2001-01-01

    Pulmonary surfactant is a multimolecular complex located at the air-water interface within the alveolus and to which a bulk of functions has been assigned, physical (surface-active properties) as well as immune or depurant. This complex consists of a surface active lipid layer (mainly phospholipids), and of an aqueous subphase. From discrete surfactant sub-fractions, one can isolate very hydrophobic proteins SP-B and SP-C as well as the collectins SP-A and SP-D, which were shown to have structural, metabolic, or defensive properties. Inborn or acquired abnormalities of surfactant, qualitative or quantitative in nature, account for a number human diseases. Beside hyaline membrane disease of the preterm neonate, a cluster of hereditary or acquired lung diseases have been characterized by the storage of periodic acid Schiff-positive material filling the alveoli. From this heterogeneous nosologic bulk, at least two discrete entities presently seem to emerge: 1) SP-B deficiency, in which an essentially proteinaceous material is stored within the alveoli, and which is a bona fide autosomal recessive Mendelian entity linked to the SFTPB gene (MIM 1786640), generally entailing neonatal respiratory distress with rapid fatal outcome, although partial or transient deficiencies have also been observed; 2) alveolar proteinosis, characterized by the storage of a mixed, protein and lipid material, and which constitutes a relatively heterogeneous clinical biological syndrome, with regards to age at onset (from the neonate through to adulthood) as well as the severity of associated signs. Murine models with a targeted mutation of the gene encoding GM-CSF (Csfgm) or the beta subunit of its receptor (Il3rbl) support the hypothesis of an abnormality of surfactant turnover in which the alveolar macrophage would be a key player. Beside SP-B deficiency, in which a near-consensus diagnostic chart can be designed, the ascertainment of other abnormalities of surfactant metabolism is not

  7. Deficiencies in structured medical abstracts.

    PubMed

    Froom, P; Froom, J

    1993-07-01

    This study was carried out to determine if the content of structured abstracts conforms with recommendations of the Ad Hoc Working Group for the critical appraisal of the medical literature as adopted by the Annals of Internal Medicine. The study design was a survey. All articles published in Annals of Internal Medicine in 1991, excluding editorials, case-reports, literature reviews, decision analysis, studies in medical education, descriptive studies of clinical and basic phenomena, and papers lacking a structured abstract, were studied. Of a total of 150 articles, 20 were excluded. The abstract and text of each article were assessed for the presence of the following items; patient selection criteria, statements concerning extrapolation of findings, need for further study, and whether or not the information should be used now. Number of refusers, drop outs and reason(s) for drop outs were assessed for intervention and prospective cohort studies only. Deficiencies of assessed items were noted in both abstracts and texts. For abstracts, patient selection criteria, numbers of refusers, number of drop outs and reason(s) for drop outs were reported in 44.6% (58/130), 3.1% (4/130), 16.9% (14/83) and 2.4% (2/83) respectively. These items were reported more frequently in the texts 87.7% (114/130), 9.2% (12/130), 60.2% (50/83) and 37.3% (31/83) respectively (p < 0.05). Statements concerning extrapolation of findings, need for further study and use of information now were also more frequent in texts than abstracts (p < 0.0001). A large number of structured abstracts published in the Annals of Internal Medicine in 1991, lack information recommended by the Ad Hoc Working Group. Our findings should not be extrapolated to other journals requiring structured abstracts. PMID:8326342

  8. Inferring climate variability from skewed proxy records

    NASA Astrophysics Data System (ADS)

    Emile-Geay, J.; Tingley, M.

    2013-12-01

    Many paleoclimate analyses assume a linear relationship between the proxy and the target climate variable, and that both the climate quantity and the errors follow normal distributions. An ever-increasing number of proxy records, however, are better modeled using distributions that are heavy-tailed, skewed, or otherwise non-normal, on account of the proxies reflecting non-normally distributed climate variables, or having non-linear relationships with a normally distributed climate variable. The analysis of such proxies requires a different set of tools, and this work serves as a cautionary tale on the danger of making conclusions about the underlying climate from applications of classic statistical procedures to heavily skewed proxy records. Inspired by runoff proxies, we consider an idealized proxy characterized by a nonlinear, thresholded relationship with climate, and describe three approaches to using such a record to infer past climate: (i) applying standard methods commonly used in the paleoclimate literature, without considering the non-linearities inherent to the proxy record; (ii) applying a power transform prior to using these standard methods; (iii) constructing a Bayesian model to invert the mechanistic relationship between the climate and the proxy. We find that neglecting the skewness in the proxy leads to erroneous conclusions and often exaggerates changes in climate variability between different time intervals. In contrast, an explicit treatment of the skewness, using either power transforms or a Bayesian inversion of the mechanistic model for the proxy, yields significantly better estimates of past climate variations. We apply these insights in two paleoclimate settings: (1) a classical sedimentary record from Laguna Pallcacocha, Ecuador (Moy et al., 2002). Our results agree with the qualitative aspects of previous analyses of this record, but quantitative departures are evident and hold implications for how such records are interpreted, and

  9. Vertically Integrated Seismological Analysis II : Inference

    NASA Astrophysics Data System (ADS)

    Arora, N. S.; Russell, S.; Sudderth, E.

    2009-12-01

    Methods for automatically associating detected waveform features with hypothesized seismic events, and localizing those events, are a critical component of efforts to verify the Comprehensive Test Ban Treaty (CTBT). As outlined in our companion abstract, we have developed a hierarchical model which views detection, association, and localization as an integrated probabilistic inference problem. In this abstract, we provide more details on the Markov chain Monte Carlo (MCMC) methods used to solve this inference task. MCMC generates samples from a posterior distribution π(x) over possible worlds x by defining a Markov chain whose states are the worlds x, and whose stationary distribution is π(x). In the Metropolis-Hastings (M-H) method, transitions in the Markov chain are constructed in two steps. First, given the current state x, a candidate next state x‧ is generated from a proposal distribution q(x‧ | x), which may be (more or less) arbitrary. Second, the transition to x‧ is not automatic, but occurs with an acceptance probability—α(x‧ | x) = min(1, π(x‧)q(x | x‧)/π(x)q(x‧ | x)). The seismic event model outlined in our companion abstract is quite similar to those used in multitarget tracking, for which MCMC has proved very effective. In this model, each world x is defined by a collection of events, a list of properties characterizing those events (times, locations, magnitudes, and types), and the association of each event to a set of observed detections. The target distribution π(x) = P(x | y), the posterior distribution over worlds x given the observed waveform data y at all stations. Proposal distributions then implement several types of moves between worlds. For example, birth moves create new events; death moves delete existing events; split moves partition the detections for an event into two new events; merge moves combine event pairs; swap moves modify the properties and assocations for pairs of events. Importantly, the rules for

  10. Eliminating iodine deficiency: obstacles and their removal.

    PubMed

    Padilla, Carmencita David; Fagela-Domingo, Carmelita

    2008-12-01

    Iodine deficiency remains a global concern for developing countries and some industrialised countries. Iodine deficiency is the most common cause of preventable mental retardation, posing a threat to the social and economic development of countries. Initiatives were developed and instituted to accelerate progress to achieve the goal of universal salt iodisation (USI). However, these efforts were not successful in eliminating iodine deficiency disorders (IDD) in some countries. Every year, 50 million children are born without the protection that iodine offers to the growing brain and body and about 18 million suffer some significant degree of mental impairment. The World Health Organization (WHO), United Nations Children's Fund (UNICEF) and non-governmental organisations assist to ensure that populations at risk have access to iodised salt. This paper will review the highlights of iodine deficiency and present the experiences in the various countries in Asia, i.e. assessments of the situation, action plans, and obstacles to implementation. PMID:19904447

  11. How Is Alpha-1 Antitrypsin Deficiency Diagnosed?

    MedlinePlus

    ... or symptoms of a serious lung condition, especially emphysema , without any obvious cause. He or she also may suspect AAT deficiency if you develop emphysema when you're 45 years old or younger. ...

  12. Office ergonomics: deficiencies in computer workstation design.

    PubMed

    Shikdar, Ashraf A; Al-Kindi, Mahmoud A

    2007-01-01

    The objective of this research was to study and identify ergonomic deficiencies in computer workstation design in typical offices. Physical measurements and a questionnaire were used to study 40 workstations. Major ergonomic deficiencies were found in physical design and layout of the workstations, employee postures, work practices, and training. The consequences in terms of user health and other problems were significant. Forty-five percent of the employees used nonadjustable chairs, 48% of computers faced windows, 90% of the employees used computers more than 4 hrs/day, 45% of the employees adopted bent and unsupported back postures, and 20% used office tables for computers. Major problems reported were eyestrain (58%), shoulder pain (45%), back pain (43%), arm pain (35%), wrist pain (30%), and neck pain (30%). These results indicated serious ergonomic deficiencies in office computer workstation design, layout, and usage. Strategies to reduce or eliminate ergonomic deficiencies in computer workstation design were suggested. PMID:17599795

  13. Netherton syndrome associated with growth hormone deficiency.

    PubMed

    Aydın, Banu Küçükemre; Baş, Firdevs; Tamay, Zeynep; Kılıç, Gürkan; Süleyman, Ayşe; Bundak, Rüveyde; Saka, Nurçin; Özkaya, Esen; Güler, Nermin; Darendeliler, Feyza

    2014-01-01

    Netherton syndrome (NS) is a rare autosomal recessive disorder characterized by ichthyosiform scaling, hair abnormalities, and variable atopic features. Mutations in the serine protease inhibitor Kazal type 5 (SPINK5) gene leading to lymphoepithelial Kazal-type-related inhibitor (LEKTI) deficiency cause NS. Growth retardation is a classic feature of NS, but growth hormone (GH) deficiency with subsequent response to GH therapy is not documented in the literature. It is proposed that a lack of inhibition of proteases due to a deficiency of LEKTI in the pituitary gland leads to the overprocessing of human GH in NS. Herein we report three patients with NS who had growth retardation associated with GH deficiency and responded well to GH therapy. PMID:24015757

  14. Genetics Home Reference: color vision deficiency

    MedlinePlus

    ... represents a group of conditions that affect the perception of color. Red-green color vision defects are ... two forms of color vision deficiency disrupt color perception but do not affect the sharpness of vision ( ...

  15. Genetics Home Reference: alpha-1 antitrypsin deficiency

    MedlinePlus

    ... and genetic modifiers of emphysema risk. Thorax. 2004 Mar;59(3):259-64. Review. Citation on PubMed ... alpha}1-antitrypsin deficiency. Arch Intern Med. 2009 Mar 23;169(6):546-50. doi: 10.1001/ ...

  16. Nursing home deficiency citations for safety

    PubMed Central

    Castle, NG; Wagner, LM; Ferguson, JC; Handler, SM

    2016-01-01

    Deficiency citations for safety violations in U.S. nursing homes from 2000 to 2007 are examined (representing a panel of 119,472 observations). Internal (i.e., operating characteristics of the facility), organizational (i.e., characteristics of the facility itself) and external (i.e., characteristics outside of the influence of the organization) factors associated with these deficiency citations are examined. The findings show that nursing homes increasingly receive deficiency citations for resident safety issues. Low staffing levels, poor quality of care, and an unfavorable Medicaid mix (occupancy and reimbursement) are associated with the likelihood of receiving deficiency citations for safety violations. In many cases, this likely influences the quality of life and quality of care of residents. PMID:21207305

  17. Living with Alpha-1 Antitrypsin Deficiency

    MedlinePlus

    ... Support Living with AAT deficiency may cause fear, anxiety, depression, and stress. Talk about how you feel ... and friends also can help relieve stress and anxiety. Let your loved ones know how you feel ...

  18. Genetics Home Reference: hereditary antithrombin deficiency

    MedlinePlus

    ... legs. This type of clot is called a deep vein thrombosis (DVT). Affected individuals also have an increased risk of ... III Deficiency Health Topic: Blood Clots Health Topic: Deep Vein Thrombosis Health Topic: Pulmonary Embolism Genetic and Rare Diseases ...

  19. Genetics Home Reference: combined pituitary hormone deficiency

    MedlinePlus

    ... People with combined pituitary hormone deficiency may have hypothyroidism, which is underactivity of the butterfly-shaped thyroid gland in the lower neck. Hypothyroidism can cause many symptoms, including weight gain and ...

  20. Genetics Home Reference: factor XIII deficiency

    MedlinePlus

    ... This protein plays a critical role in the coagulation cascade, which is a series of chemical reactions ... Biswas A, Ivaskevicius V, Thomas A, Oldenburg J. Coagulation factor XIII deficiency. Diagnosis, prevalence and management of ...