Efficient Learning of the Parameters of Non-Linear Models using Differentiable Resampling in Particle Filters

It has been widely documented that the sampling and resampling steps in particle filters cannot be differentiated. The {\itshape reparameterisation trick} was introduced to allow the sampling step to be reformulated into a differentiable function. We extend the {\itshape reparameterisation trick} to include the stochastic input to resampling therefore limiting the discontinuities in the gradient calculation after this step. Knowing the gradients of the prior and likelihood allows us to run particle Markov Chain Monte Carlo (p-MCMC) and use the No-U-Turn Sampler (NUTS) as the proposal when estimating parameters. We compare the Metropolis-adjusted Langevin algorithm (MALA), Hamiltonian Monte Carlo with different number of steps and NUTS. We consider two state-space models and show that NUTS improves the mixing of the Markov chain and can produce more accurate results in less computational time.Comment: 35 pages, 10 figure

Surface topography of hydroxyapatite affects ROS17/2.8 cells response

A hidroxiapatita (HA) tem sido utilizada como revestimento de implantes e para substituição de tecido ósseo. O objetivo deste estudo foi avaliar o efeito da topografia de superfície da HA, resultante da presença de microporosidade, sobre a adesão, a morfologia e proliferação celulares, a medida de proteína total e a atividade de fosfatase alcalina. Discos de HA com diferentes porcentagens de microporosidade (< 5%, 15% e 30%) foram fabricados por uma combinação das técnicas de pressão uniaxial e sinterização. Células ROS17/2.8 foram cultivadas sobre os discos de HA. Para a adesão, as células foram cultivadas por duas horas. A morfologia foi avaliada após sete dias. A proliferação, medida de proteína total e atividade de ALP foram avaliadas após sete e quatorze dias. Os dados foram comparados por ANOVA e teste de Duncan quando apropriado. A adesão (p = 0,11) e a medida de proteína total (p = 0,31) não foram afetadas pela topografia de superfície. A proliferação após sete e quatorze dias (p = 0,0007 e p = 0,003, respectivamente), e a atividade de ALP (p = 0,0007) foram significantemente menores na superfície irregular (HA30). Esses resultados sugerem que eventos iniciais não são afetados pela topografia, enquanto superfícies com topografias mais regulares (microporosidade de 15% ou menos) favoreceram eventos intermediários e finais, como proliferação e atividade de ALP.Hydroxyapatite (HA) has been used in orthopedic, dental, and maxillofacial surgery as a bone substitute. The aim of this investigation was to study the effect of surface topography produced by the presence of microporosity on cell response, evaluating: cell attachment, cell morphology, cell proliferation, total protein content, and alkaline phosphatase (ALP) activity. HA discs with different percentages of microporosity (< 5%, 15%, and 30%) were confected by means of the combination of uniaxial powder pressing and different sintering conditions. ROS17/2.8 cells were cultured on HA discs. For the evaluation of attachment, cells were cultured for two hours. Cell morphology was evaluated after seven days. After seven and fourteen days, cell proliferation, total protein content, and ALP activity were measured. Data were compared by means of ANOVA and Duncans multiple range test, when appropriate. Cell attachment (p = 0.11) and total protein content (p = 0.31) were not affected by surface topography. Proliferation after 7 and 14 days (p = 0.0007 and p = 0.003, respectively), and ALP activity (p = 0.0007) were both significantly decreased by the most irregular surface (HA30). These results suggest that initial cell events were not affected by surface topography, while surfaces with more regular topography, as those present in HA with 15% or less of microporosity, favored intermediary and final events such as cell proliferation and ALP activity

QueryForm: A Simple Zero-shot Form Entity Query Framework

Zero-shot transfer learning for document understanding is a crucial yet under-investigated scenario to help reduce the high cost involved in annotating document entities. We present a novel query-based framework, QueryForm, that extracts entity values from form-like documents in a zero-shot fashion. QueryForm contains a dual prompting mechanism that composes both the document schema and a specific entity type into a query, which is used to prompt a Transformer model to perform a single entity extraction task. Furthermore, we propose to leverage large-scale query-entity pairs generated from form-like webpages with weak HTML annotations to pre-train QueryForm. By unifying pre-training and fine-tuning into the same query-based framework, QueryForm enables models to learn from structured documents containing various entities and layouts, leading to better generalization to target document types without the need for target-specific training data. QueryForm sets new state-of-the-art average F1 score on both the XFUND (+4.6%~10.1%) and the Payment (+3.2%~9.5%) zero-shot benchmark, with a smaller model size and no additional image input.Comment: Accepted to Findings of ACL 202

Exocytosis of acid sphingomyelinase by wounded cells promotes endocytosis and plasma membrane repair

Lysosomal enzyme acid sphingomyelinase is released extracellularly when cells are wounded, converting sphingomyelin to ceramide and inducing endosome formation to internalize membrane lesions

Surface topography of hydroxyapatite affects ROS17/2.8 cells response

Hydroxyapatite (HA) has been used in orthopedic, dental, and maxillofacial surgery as a bone substitute. The aim of this investigation was to study the effect of surface topography produced by the presence of microporosity on cell response, evaluating: cell attachment, cell morphology, cell proliferation, total protein content, and alkaline phosphatase (ALP) activity. HA discs with different percentages of microporosity (< 5%, 15%, and 30%) were confected by means of the combination of uniaxial powder pressing and different sintering conditions. ROS17/2.8 cells were cultured on HA discs. For the evaluation of attachment, cells were cultured for two hours. Cell morphology was evaluated after seven days. After seven and fourteen days, cell proliferation, total protein content, and ALP activity were measured. Data were compared by means of ANOVA and Duncan’s multiple range test, when appropriate. Cell attachment (p = 0.11) and total protein content (p = 0.31) were not affected by surface topography. Proliferation after 7 and 14 days (p = 0.0007 and p = 0.003, respectively), and ALP activity (p = 0.0007) were both significantly decreased by the most irregular surface (HA30). These results suggest that initial cell events were not affected by surface topography, while surfaces with more regular topography, as those present in HA with 15% or less of microporosity, favored intermediary and final events such as cell proliferation and ALP activity

Maternal milk consumption, fetal growth, and the risks of neonatal complications: The Generation R Study

Background: Maternal cow-milk consumption may increase birth weight. Previous studies did not assess the association of maternal milk consumption with trimester-specific fetal growth. Objective: The objective was to assess associations of first-trimester maternal milk consumption with fetal growth characteristics in different trimesters and the risk of neonatal complications. Design: In total, 3405 mothers participating in a prospective cohort study completed a 293-item semiquantitative food-frequency questionnaire to obtain information about dairy consumption during the first trimester of pregnancy. Fetal head circumference, femur length, and weight were estimated in the second and third trimesters by ultrasonography. Results: Maternal milk consumption of >3 glasses/d was associated with greater fetal weight gain in the third trimester of pregnancy, which led to an 88-g (95% CI: 39, 135 g) higher birth weight than that with milk consumption of 0 to 1 glass/d. In addition, head circumference tended to be 2.3 cm (95% CI: -0.0, 4.6 cm) larger when mothers consumed >3 glasses/d. Maternal milk consumption was not associated with length growth. Maternal protein intake (P for trend = 0.01), but not fat or carbohydrate intake, from dairy products was associated with higher birth weight. This association appeared to be limited to milk (P for trend < 0.01), whereas protein intake from nondairy food or cheese was not associated with birth weight. Conclusions: Maternal milk consumption is associated with greater fetal weight gain. The association seems to be due to milk protein, or milk components closely associated with protein, rather than to the fat or carbohydrate fraction of milk

A genome-wide scan for common alleles affecting risk for autism

Although autism spectrum disorders (ASDs) have a substantial genetic basis, most of the known genetic risk has been traced to rare variants, principally copy number variants (CNVs). To identify common risk variation, the Autism Genome Project (AGP) Consortium genotyped 1558 rigorously defined ASD families for 1 million single-nucleotide polymorphisms (SNPs) and analyzed these SNP genotypes for association with ASD. In one of four primary association analyses, the association signal for marker rs4141463, located within MACROD2, crossed the genome-wide association significance threshold of P < 5 × 10−8. When a smaller replication sample was analyzed, the risk allele at rs4141463 was again over-transmitted; yet, consistent with the winner's curse, its effect size in the replication sample was much smaller; and, for the combined samples, the association signal barely fell below the P < 5 × 10−8 threshold. Exploratory analyses of phenotypic subtypes yielded no significant associations after correction for multiple testing. They did, however, yield strong signals within several genes, KIAA0564, PLD5, POU6F2, ST8SIA2 and TAF1C

Rapid Pliocene exhumation of the central Greater Caucasus constrained by low‐temperature thermochronometry

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/94839/1/tect2241.pd

Hundreds of variants clustered in genomic loci and biological pathways affect human height

Most common human traits and diseases have a polygenic pattern of inheritance: DNA sequence variants at many genetic loci influence the phenotype. Genome-wide association (GWA) studies have identified more than 600 variants associated with human traits, but these typically explain small fractions of phenotypic variation, raising questions about the use of further studies. Here, using 183,727 individuals, we show that hundreds of genetic variants, in at least 180 loci, influence adult height, a highly heritable and classic polygenic trait. The large number of loci reveals patterns with important implications for genetic studies of common human diseases and traits. First, the 180 loci are not random, but instead are enriched for genes that are connected in biological pathways (P = 0.016) and that underlie skeletal growth defects (P < 0.001). Second, the likely causal gene is often located near the most strongly associated variant: in 13 of 21 loci containing a known skeletal growth gene, that gene was closest to the associated variant. Third, at least 19 loci have multiple independently associated variants, suggesting that allelic heterogeneity is a frequent feature of polygenic traits, that comprehensive explorations of already-discovered loci should discover additional variants and that an appreciable fraction of associated loci may have been identified. Fourth, associated variants are enriched for likely functional effects on genes, being over-represented among variants that alter amino-acid structure of proteins and expression levels of nearby genes. Our data explain approximately 10% of the phenotypic variation in height, and we estimate that unidentified common variants of similar effect sizes would increase this figure to approximately 16% of phenotypic variation (approximately 20% of heritable variation). Although additional approaches are needed to dissect the genetic architecture of polygenic human traits fully, our findings indicate that GWA studies can identify large numbers of loci that implicate biologically relevant genes and pathways.