MissForest - nonparametric missing value imputation for mixed-type data

Modern data acquisition based on high-throughput technology is often facing the problem of missing data. Algorithms commonly used in the analysis of such large-scale data often depend on a complete set. Missing value imputation offers a solution to this problem. However, the majority of available imputation methods are restricted to one type of variable only: continuous or categorical. For mixed-type data the different types are usually handled separately. Therefore, these methods ignore possible relations between variable types. We propose a nonparametric method which can cope with different types of variables simultaneously. We compare several state of the art methods for the imputation of missing values. We propose and evaluate an iterative imputation method (missForest) based on a random forest. By averaging over many unpruned classification or regression trees random forest intrinsically constitutes a multiple imputation scheme. Using the built-in out-of-bag error estimates of random forest we are able to estimate the imputation error without the need of a test set. Evaluation is performed on multiple data sets coming from a diverse selection of biological fields with artificially introduced missing values ranging from 10% to 30%. We show that missForest can successfully handle missing values, particularly in data sets including different types of variables. In our comparative study missForest outperforms other methods of imputation especially in data settings where complex interactions and nonlinear relations are suspected. The out-of-bag imputation error estimates of missForest prove to be adequate in all settings. Additionally, missForest exhibits attractive computational efficiency and can cope with high-dimensional data.Comment: Submitted to Oxford Journal's Bioinformatics on 3rd of May 201

Chromospheric polarimetry through multi-line observations of the 850 nm spectral region

Future solar missions and ground-based telescopes aim to understand the magnetism of the solar chromosphere. We performed a supporting study in Quintero Noda et al. (2016) focused on the infrared Ca II 8542 A line and we concluded that is one of the best candidates because it is sensitive to a large range of atmospheric heights, from the photosphere to the middle chromosphere. However, we believe that it is worth to try improving the results produced by this line observing additional spectral lines. In that regard, we examined the neighbour solar spectrum looking for spectral lines that could increase the sensitivity to the atmospheric parameters. Interestingly, we discovered several photospheric lines that greatly improve the photospheric sensitivity to the magnetic field vector. Moreover, they are located close to a second chromospheric line that also belongs to the Ca II infrared triplet, i.e. the Ca II 8498 A line, and enhances the sensitivity to the atmospheric parameters at chromospheric layers. We conclude that the lines in the vicinity of the Ca II 8542 A line not only increase its sensitivity to the atmospheric parameters at all layers, but also they constitute an excellent spectral window for chromospheric polarimetry.Comment: 11 pages, 8 figures, 1 tabl

Cross-polarized optical absorption of single-walled nanotubes probed by polarized photoluminescence excitation spectroscopy

Cross-polarized absorption peaks of isolated single-walled carbon nanotubes were observed by a polarized photoluminescence excitation (PLE) spectroscopy. Using a simple theory for PL anisotropy, the observed PLE spectra are decomposed into 'pure' components of the photoexcitation for incident light polarized parallel and perpendicular to the SWNT axis. For several (n, m) SWNTs, distinct peaks corresponding to perpendicular excitation were observed. The measured transition energies for perpendicular excitations were blue-shifted compared to the qualitative values predicted within a single-particle theory. The results indicate a smaller exciton binding energy for perpendicular excitations than for parallel excitations.Comment: 7 pages, 5 figures, submitted to Phys. Rev.

Use of Stockpiled Berseem Clover as a Supplement for Grazed Corn Crop Residues

In the fall of 1994, mature Charolais cross cows in midgestation were allotted to duplicate 15 acre fields containing corn crop residues or a 2-to-1 mixture of corn crop residues and berseem clover planted in 3 strips at an allowance of 2.5 acres/cow for a 140 day wintering season. Similar cows were allotted duplicate drylots. All cows were fed hay as necessary to maintain a body condition score of 5. Cows grazing corn crop residues with or without berseem clover required 2596 pounds less hay per cow than cows maintained in a drylot. There was no difference in the amounts of hay required by cows grazing corn crop residues alone or with berseem clover. Initial organic matter yield of berseem clover was nearly that of corn crop residues and did not decrease as rapidly as corn crop residues. Berseem clover had a higher organic matter digestibility than corn crop residues at the initiation of grazing. Organic matter digestibility of berseem clover, however, decreased more rapidly than corn crop residues because of weathering during the winter

Relative Cost-effectiveness Of Using An Extensively Hydrolyzed Casein Formula In Managing Infants With Cow’s Milk Allergy In Brazil

To estimate the cost-effectiveness of three alternative dietetic strategies for cow’s milk allergy in Brazil: 1) using an extensively hydrolyzed casein formula (eHCF; Nutramigen) as a first-line formula, but switching to an amino acid formula (AAF) if infants remain symptomatic; 2) using an AAF as a first-line formula and then switching to an eHCF after 4 weeks once infants are symptom-free, but switching back to an AAF if infants become symptomatic; and 3) using an AAF as a first-line formula and keeping all infants on that formula. The analysis was conducted from the perspective of the Brazilian public health care system, Sistema Único de Saude. Methods: Decision modeling was used to estimate the probability of immunoglobulin E (IgE)-mediated and non-IgE-mediated allergic infants developing tolerance to cow’s milk by 12 months from starting a formula. The models also estimated the Sistema Único de Saude cost (at 2013/2014 prices) of managing infants over 12 months after starting a formula, as well as the relative cost-effectiveness of each of the dietetic strategies. Results: The probability of developing tolerance to cow’s milk by 12 months from starting a formula was higher among infants with either IgE-mediated or non-IgE-mediated allergy who were initially fed with an eHCF, compared with those who were initially fed with an AAF. The total health care cost of initially feeding an eHCF to cow’s milk allergic infants was less than that of initially feeding both IgE-mediated and non-IgE-mediated infants with an AAF. Conclusion: Within the study’s limitations, using an eHCF instead of an AAF for the first-line management of newly-diagnosed infants with cow’s milk allergy affords a cost-effective use of publicly funded resources, since it improves the outcome for less cost. © 2016 Guest et al.862963

Chromospheric polarimetry through multi-line observations of the 850 nm spectral region II: A magnetic flux tube scenario

In this publication we continue the work started in Quintero Noda et al. (2017) examining this time a numerical simulation of a magnetic flux tube concentration. Our goal is to study if the physical phenomena that take place in it, in particular, the magnetic pumping, leaves a specific imprint on the examined spectral lines. We find that the profiles from the interior of the flux tube are periodically dopplershifted following an oscillation pattern that is also reflected in the amplitude of the circular polarization signals. In addition, we analyse the properties of the Stokes profiles at the edges of the flux tube discovering the presence of linear polarization signals for the Ca II lines, although they are weak with an amplitude around 0.5% of the continuum intensity. Finally, we compute the response functions to perturbations in the longitudinal field and we estimate the field strength using the weak field approximation. Our results indicate that the height of formation of the spectral lines changes during the magnetic pumping process which makes the interpretation of the inferred magnetic field strength and its evolution more difficult. These results complement those from previous works demonstrating the capabilities and limitations of the 850 nm spectrum for chromospheric Zeeman polarimetry in a very dynamic and complex atmosphere.Comment: 12 pages, 12 figures, 0 tables, MNRAS main journal publicatio

Chromospheric polarimetry through multi-line observations of the 850 nm spectral region III: Chromospheric jets driven by twisted magnetic fields

We investigate the diagnostic potential of the spectral lines at 850 nm for understanding the magnetism of the lower atmosphere. For that purpose, we use a newly developed 3D simulation of a chromospheric jet to check the sensitivity of the spectral lines to this phenomenon as well as our ability to infer the atmospheric information through spectropolarimetric inversions of noisy synthetic data. We start comparing the benefits of inverting the entire spectrum at 850 nm versus only the Ca II 8542 A spectral line. We found a better match of the input atmosphere for the former case, mainly at lower heights. However, the results at higher layers were not accurate. After several tests, we determined that we need to weight more the chromospheric lines than the photospheric ones in the computation of the goodness of the fit. The new inversion configuration allows us to obtain better fits and consequently more accurate physical parameters. Therefore, to extract the most from multi-line inversions, a proper set of weights needs to be estimated. Besides that, we conclude again that the lines at 850 nm, or a similar arrangement with Ca II 8542 A plus Zeeman sensitive photospheric lines, poses the best observing configuration for examining the thermal and magnetic properties of the lower solar atmosphere.Comment: 14 pages, 11 figure

Stephanofilaria sp em bovinos do município de São Carlos, Estado de São Paulo.

Estudos clínicas e laboratórios em ulceras do tipo "Chagas de Verão" em bovinos do Município de São Carlos. Observou-se uma dermatite nodular ulcerativa na região da quartela, jarrete, cruz, cabeça, teta, paleta

Reproductive parameters of dairy goats submitted to estrus synchronization with prostaglandin F2alfa associated or not to hCG at estrous onset.

Abstract: The objective of this study was to evaluate the efficiency of two doses of PGF associated or not to hCG on the associated reproductive parameters in dairy goats. A total of 29 goats received two doses of 30 ug d-cloprostenol latero-vulvar at a 10 day intervals (Day 1 and Day 10). The does were allocated according to body weight and body condition score into two treatments, to receive hCG (250IU) or saline at estrus onset. After the second dose of PGF, estrus was monitored and ultrasound exams were performed twice daily. All does were inseminated 16h after estrus onset. Blood collection was performed every day for progesterone assay. The use of hCG at estrus onset did not affect any studied parameter and therefore the data were pooled. Estrous response rate was similar (P>0.05) after the first (75.9%, 22/29) and the second dose of PGF (79.3%, 23/29). The interval between the administration of PGF and estrus onset was greater (P0.05) between both experimental groups were detected in the following parameters, averaging: the interval from the second dose administration to the ovulation (86.6±11.4h), interval from estrus to ovulation (39.9±12.3 h), diameter of largest follicle (7.2±1.4) and number of ovulations (1.8±0.6). At Day 1, 52.4% (11/21) of does presented progesterone concentrations 1ng/mL. The results of the present study indicate that estrus can be efficiently synchronized in dairy goats with the use of two doses of PGF at a 10 day interval. Further research should be done evaluating hCG use in different doses or moments of administration. [Parâmetros ovarianos de cabras leiteira submetidas a sincronização do estro com protaglandina F2 alfa associada ou não ao hCG no início do estro]. Resumo: O objetivo deste estudo foi avaliar a eficiência do uso de duas doses de PGF associadas ou não à administração de hCG no início do estro sobre os parâmetros reprodutivos de cabras leiteiras. Um total de 29 cabras receberam duas doses de 30 ?g d-cloprostenol pela via latero-vulvar com 10 dias de intervalo (Dia 1 e Dia 10). As cabras foram alocadas para receberem o hCG (250 IU) ou salina i.m. no momento em que o estro foi detectado. Depois da realização da segunda dose de PGF, o estro foi monitorado e exames ultrassonográficos foram realizados duas vezes ao dia. Todas as fêmeas foram inseminadas 16 h após o inicio do estro. Amostras de sangue foram coletadas diariamente para determinação das concentrações plasmáticas de progesterona. O uso do hCG no momento do início do estro não afetou os parâmetros estudados e, portanto, os dados serão apresentados agrupados. A taxa de manifestação de estro foi similar (P > 0,05) na primeira (75,9% - 22/29) ou na segunda dose de PGF (79,3% - 23/29). O intervalo entre a administração de PGF e o início do estro foi maior (P 0,05) entre os grupos experimentais quanto aos parâmetros reprodutivos: intervalo entre a aplicação da segunda dose e a ovulação (86,6±11,4h), intervalo do estro a ocorrência da ovulação (39,9±12,3h), diâmetro do maior folículo (7,2±1,4) e número de ovulações (1,8±0,6). No Dia 1, 52,4% (11/21) apresentavam concentrações de progesterona 1ng/mL. O presente estudo permite concluir que o estro pode ser eficientemente sincronizado em cabras leiteiras com duas doses de PGF intervaladas em 10 dias. Novas pesquisas devem se realizadas para avaliar diferentes doses e momentos de utilização do hCG