Robust Inference of Trees

This paper is concerned with the reliable inference of optimal tree-approximations to the dependency structure of an unknown distribution generating data. The traditional approach to the problem measures the dependency strength between random variables by the index called mutual information. In this paper reliability is achieved by Walley's imprecise Dirichlet model, which generalizes Bayesian learning with Dirichlet priors. Adopting the imprecise Dirichlet model results in posterior interval expectation for mutual information, and in a set of plausible trees consistent with the data. Reliable inference about the actual tree is achieved by focusing on the substructure common to all the plausible trees. We develop an exact algorithm that infers the substructure in time O(m^4), m being the number of random variables. The new algorithm is applied to a set of data sampled from a known distribution. The method is shown to reliably infer edges of the actual tree even when the data are very scarce, unlike the traditional approach. Finally, we provide lower and upper credibility limits for mutual information under the imprecise Dirichlet model. These enable the previous developments to be extended to a full inferential method for trees.Comment: 26 pages, 7 figure

Tail and ear necrosis in piglets of sows with increased weight loss over the suckling period.

A farm belonging to a Swiss sow pool system reported increased cases of necrosis on the base of the tail or ears in their piglets. Therefore, herd examination was performed in February 2021, and it was found that about half of all examined litters included piglets with necrosis of different locations, and that the sows of these piglets were rather thin. Upon instruction, the farmer then documented the body condition score (BCS) and weight before farrowing and after weaning, and the number of liveborn piglets affected by necrosis of the tail or ear of the next four farrowing batches. In total, data of 97 sows with 1214 liveborn piglets were evaluated. Sows were retrospectively allocated into two groups: Those with piglets with ear and/or tail necrosis (NE), and those without (WN). Of the 97 litters, 40 included piglets with necrosis, with 28 of them having piglets only with tail necrosis, 8 only with ear necrosis, and 4 litters included piglets with both types of necrosis. The group NE lost significantly more weight and BCS points over the suckling period than the group WN, with a tendency of having a lower BCS after weaning (2,0 vs. 2,25/5,0). Blood samples of five sows were analyzed and tested positive for the Fusarium mycotoxin deoxynivalenol (DON). It could be possible that the sows previously consumed DON contaminated feed, which was then stored in their fat tissue, and released again into the blood stream during increased weight loss. Since DON can be transferred from the sow to her piglets during gestation or lactation, this release might have affected the piglets, leading to tail or ear necrosis. However, causative studies are needed to confirm this hypothesis

A case of Muir-Torre syndrome associated with mucinous hepatic cholangiocarcinoma and a novel germline mutation of the MSH2 gene

Muir-Torre syndrome (MTS) is a rare cancer-predisposing syndrome that is autosomal dominantly inherited and characterized by the development of sebaceous skin lesions (adenomas, epitheliomas, basaliomas and carcinomas). These lesions are typically associated with tumors that belong to the spectrum of hereditary nonpolyposis colorectal cancer (HNPCC) (i.e. tumors of the colorectum, endometrium, stomach or ovary). Biliary malignancy in association with MTS has only rarely been reported. We report a case of Muir-Torre syndrome associated with intrahepatic cholangiocarcinoma, a location not previously described, and associated with a novel missense mutation of the MSH2 gene (c.2026T>C), predicted to disrupt the function of the gen

Bayesian DNA copy number analysis

<p>Abstract</p> <p>Background</p> <p>Some diseases, like tumors, can be related to chromosomal aberrations, leading to changes of DNA copy number. The copy number of an aberrant genome can be represented as a piecewise constant function, since it can exhibit regions of deletions or gains. Instead, in a healthy cell the copy number is two because we inherit one copy of each chromosome from each our parents.</p> <p>Bayesian Piecewise Constant Regression (BPCR) is a Bayesian regression method for data that are noisy observations of a piecewise constant function. The method estimates the unknown segment number, the endpoints of the segments and the value of the segment levels of the underlying piecewise constant function. The Bayesian Regression Curve (BRC) estimates the same data with a smoothing curve. However, in the original formulation, some estimators failed to properly determine the corresponding parameters. For example, the boundary estimator did not take into account the dependency among the boundaries and succeeded in estimating more than one breakpoint at the same position, losing segments.</p> <p>Results</p> <p>We derived an improved version of the BPCR (called mBPCR) and BRC, changing the segment number estimator and the boundary estimator to enhance the fitting procedure. We also proposed an alternative estimator of the variance of the segment levels, which is useful in case of data with high noise. Using artificial data, we compared the original and the modified version of BPCR and BRC with other regression methods, showing that our improved version of BPCR generally outperformed all the others. Similar results were also observed on real data.</p> <p>Conclusion</p> <p>We propose an improved method for DNA copy number estimation, mBPCR, which performed very well compared to previously published algorithms. In particular, mBPCR was more powerful in the detection of the true position of the breakpoints and of small aberrations in very noisy data. Hence, from a biological point of view, our method can be very useful, for example, to find targets of genomic aberrations in clinical cancer samples.</p

Cerebral Microdialysate Metabolite Monitoring using Mid-infrared Spectroscopy.

Funder: Wellcome TrustThe brains of patients suffering from traumatic brain-injury (TBI) undergo dynamic chemical changes in the days following the initial trauma. Accurate and timely monitoring of these changes is of paramount importance for improved patient outcome. Conventional brain-chemistry monitoring is performed off-line by collecting and manually transferring microdialysis samples to an enzymatic colorimetric bedside analyzer every hour, which detects and quantifies the molecules of interest. However, off-line, hourly monitoring means that any subhourly neurochemical changes, which may be detrimental to patients, go unseen and thus untreated. Mid-infrared (mid-IR) spectroscopy allows rapid, reagent-free, molecular fingerprinting of liquid samples, and can be easily integrated with microfluidics. We used mid-IR transmission spectroscopy to analyze glucose, lactate, and pyruvate, three relevant brain metabolites, in the extracellular brain fluid of two TBI patients, sampled via microdialysis. Detection limits of 0.5, 0.2, and 0.1 mM were achieved for pure glucose, lactate, and pyruvate, respectively, in perfusion fluid using an external cavity-quantum cascade laser (EC-QCL) system with an integrated transmission flow-cell. Microdialysates were collected hourly, then pooled (3-4 h), and measured consecutively using the standard ISCUSflex analyzer and the EC-QCL system. There was a strong correlation between the compound concentrations obtained using the conventional bedside analyzer and the acquired mid-IR absorbance spectra, where a partial-least-squares regression model was implemented to compute concentrations. This study demonstrates the potential utility of mid-IR spectroscopy for continuous, automated, reagent-free, and online monitoring of the dynamic chemical changes in TBI patients, allowing a more timely response to adverse brain metabolism and consequently improving patient outcomes

Constraining Disk Parameters of Be Stars using Narrowband H-alpha Interferometry with the NPOI

Interferometric observations of two well-known Be stars, gamma Cas and phi Per, were collected and analyzed to determine the spatial characteristics of their circumstellar regions. The observations were obtained using the Navy Prototype Optical Interferometer equipped with custom-made narrowband filters. The filters isolate the H-alpha emission line from the nearby continuum radiation, which results in an increased contrast between the interferometric signature due to the H-alpha-emitting circumstellar region and the central star. Because the narrowband filters do not significantly attenuate the continuum radiation at wavelengths 50 nm or more away from the line, the interferometric signal in the H-alpha channel is calibrated with respect to the continuum channels. The observations used in this study represent the highest spatial resolution measurements of the H-alpha-emitting regions of Be stars obtained to date. These observations allow us to demonstrate for the first time that the intensity distribution in the circumstellar region of a Be star cannot be represented by uniform disk or ring-like structures, whereas a Gaussian intensity distribution appears to be fully consistent with our observations.Comment: 23 pages, 14 figures, accepted for publication in A

The strong coupling constant at small momentum as an instanton detector

We present a study of $\alpha_{MOM}(p)$ at small p computed from the lattice. It shows a dramatic $\propto p^4$ law which can be understood within an instanton liquid model. In this framework the prefactor gives a direct measure of the instanton density in thermalised configurations. A preliminary result for this density is 5.27(4) fm^{-4}.Comment: 12 pages, 4 figure

Inpatient and outpatient costs in patients with coronary artery disease and mental disorders: a systematic review

Background: To systematically review in- and outpatient costs in patients with coronary artery disease (CAD) and comorbid mental disorders. Methods: A comprehensive database search was conducted for studies investigating persons with CAD and comorbid mental disorders (Medline, EMBASE, PsycINFO, Psyndex, EconLit, IBSS). All studies were included which allowed a comparison of in- and outpatient health care costs (assessed either monetarily or in terms of health care utilization) of CAD patients with comorbid mental disorders (mood, anxiety, alcohol, eating, somatoform and personality disorders) and those without. Random effects meta-analyses were conducted and results reported using forest plots. Results: The literature search resulted in 7,275 potentially relevant studies, of which 52 met inclusion criteria. Hospital readmission rates were increased in CAD patients with any mental disorder (pooled standardized mean difference (SMD) = 0.34 [0.17;0.51]). Results for depression, anxiety and posttraumatic stress disorder pointed in the same direction with heterogeneous SMDs on a primary study level ranging from -0.44 to 1.26. Length of hospital stay was not increased in anxiety and any mental disorder, while studies on depression reported heterogeneous SMDs ranging from -0.08 to 0.82. Most studies reported increased overall and outpatient costs for patients with comorbid mental disorders. Results for invasive procedures were non-significant respectively inconclusive. Conclusions: Comorbid mental disorders in CAD patients are associated with an increased healthcare utilization in terms of higher hospital readmission rates and increased overall and outpatient health care costs. From a health care point of view, it is requisite to improve the diagnosis and treatment of comorbid mental disorders in patients with CAD to minimize incremental costs.Harald Baumeister, Anne Haschke, Marie Munzinger, Nico Hutter, and Phillip J Tull

Salmeterol for the prevention of high-altitude pulmonary edema.

BACKGROUND: Pulmonary edema results from a persistent imbalance between forces that drive water into the air space and the physiologic mechanisms that remove it. Among the latter, the absorption of liquid driven by active alveolar transepithelial sodium transport has an important role; a defect of this mechanism may predispose patients to pulmonary edema. Beta-adrenergic agonists up-regulate the clearance of alveolar fluid and attenuate pulmonary edema in animal models. METHODS: In a double-blind, randomized, placebo-controlled study, we assessed the effects of prophylactic inhalation of the beta-adrenergic agonist salmeterol on the incidence of pulmonary edema during exposure to high altitudes (4559 m, reached in less than 22 hours) in 37 subjects who were susceptible to high-altitude pulmonary edema. We also measured the nasal transepithelial potential difference, a marker of the transepithelial sodium and water transport in the distal airways, in 33 mountaineers who were prone to high-altitude pulmonary edema and 33 mountaineers who were resistant to this condition. RESULTS: Prophylactic inhalation of salmeterol decreased the incidence of high-altitude pulmonary edema in susceptible subjects by more than 50 percent, from 74 percent with placebo to 33 percent (P=0.02). The nasal potential-difference value under low-altitude conditions was more than 30 percent lower in the subjects who were susceptible to high-altitude pulmonary edema than in those who were not susceptible (P&lt;0.001). CONCLUSIONS: Prophylactic inhalation of a beta-adrenergic agonist reduces the risk of high-altitude pulmonary edema. Sodium-dependent absorption of liquid from the airways may be defective in patients who are susceptible to high-altitude pulmonary edema. These findings support the concept that sodium-driven clearance of alveolar fluid may have a pathogenic role in pulmonary edema in humans and therefore represent an appropriate target for therapy