Improving predictive performance on survival in dairy cattle using an ensemble learning approach

Cow survival is a complex trait that combines traits like milk production, fertility, health and environmental factors such as farm management. This complexity makes survival difficult to predict accurately. This is probably the reason why few studies attempted to address this problem and no studies are published that use ensemble methods for this purpose. We explored if we could improve prediction of cow survival to second lactation, when predicted at five different moments in a cow's life, by combining the predictions of multiple (weak) methods in an ensemble method. We tested four ensemble methods: majority voting rule, multiple logistic regression, random forest and naive Bayes. Precision, recall, balanced accuracy, area under the curve (AUC) and gains in proportion of surviving cows in a scenario where the best 50% were selected were used to evaluate the ensemble model performance. We also calculated correlations between the ensemble models and obtained McNemar's test statistics. We compared the performance of the ensemble methods against those of the individual methods. We also tested if there was a difference in performance metrics when continuous (from 0 to 1) and binary (0 or 1) prediction outcomes were used. In general, using continuous prediction output resulted in higher performance metrics than binary ones. AUCs for models ranged from 0.561 to 0.731, with generally increasing performance at moments later in life. Precision, AUC and balanced accuracy values improved significantly for the naive Bayes and multiple logistic regression ensembles in at least one data set, although performance metrics did remain low overall. The multiple logistic regression ensemble method resulted in equal or better precision, AUC, balanced accuracy and proportion of animals surviving on all datasets and was significantly different from the other ensembles in three out of five moments. The random forest ensemble method resulted in the least significant improvement over the individual methods

Lyashko-Looijenga morphisms and submaximal factorisations of a Coxeter element

When W is a finite reflection group, the noncrossing partition lattice NCP_W of type W is a rich combinatorial object, extending the notion of noncrossing partitions of an n-gon. A formula (for which the only known proofs are case-by-case) expresses the number of multichains of a given length in NCP_W as a generalised Fuss-Catalan number, depending on the invariant degrees of W. We describe how to understand some specifications of this formula in a case-free way, using an interpretation of the chains of NCP_W as fibers of a Lyashko-Looijenga covering (LL), constructed from the geometry of the discriminant hypersurface of W. We study algebraically the map LL, describing the factorisations of its discriminant and its Jacobian. As byproducts, we generalise a formula stated by K. Saito for real reflection groups, and we deduce new enumeration formulas for certain factorisations of a Coxeter element of W.Comment: 18 pages. Version 2 : corrected typos and improved presentation. Version 3 : corrected typos, added illustrated example. To appear in Journal of Algebraic Combinatoric

RNA editing signature during myeloid leukemia cell differentiation

Adenosine deaminases acting on RNA (ADARs) are key proteins for hematopoietic stem cell self-renewal and for survival of differentiating progenitor cells. However, their specific role in myeloid cell maturation has been poorly investigated. Here we show that ADAR1 is present at basal level in the primary myeloid leukemia cells obtained from patients at diagnosis as well as in myeloid U-937 and THP1 cell lines and its expression correlates with the editing levels. Upon phorbol-myristate acetate or Vitamin D3/granulocyte macrophage colony-stimulating factor (GM-CSF)-driven differentiation, both ADAR1 and ADAR2 enzymes are upregulated, with a concomitant global increase of A-to-I RNA editing. ADAR1 silencing caused an editing decrease at specific ADAR1 target genes, without, however, interfering with cell differentiation or with ADAR2 activity. Remarkably, ADAR2 is absent in the undifferentiated cell stage, due to its elimination through the ubiquitin–proteasome pathway, being strongly upregulated at the end of the differentiation process. Of note, peripheral blood monocytes display editing events at the selected targets similar to those found in differentiated cell lines. Taken together, the data indicate that ADAR enzymes play important and distinct roles in myeloid cells

Unimodality Problems in Ehrhart Theory

Ehrhart theory is the study of sequences recording the number of integer points in non-negative integral dilates of rational polytopes. For a given lattice polytope, this sequence is encoded in a finite vector called the Ehrhart $h^*$-vector. Ehrhart $h^*$-vectors have connections to many areas of mathematics, including commutative algebra and enumerative combinatorics. In this survey we discuss what is known about unimodality for Ehrhart $h^*$-vectors and highlight open questions and problems.Comment: Published in Recent Trends in Combinatorics, Beveridge, A., et al. (eds), Springer, 2016, pp 687-711, doi 10.1007/978-3-319-24298-9_27. This version updated October 2017 to correct an error in the original versio

Mitigating Climate Biases in the Midlatitude North Atlantic by Increasing Model Resolution: SST Gradients and Their Relation to Blocking and the Jet

Starting to resolve the oceanic mesoscale in climate models is a step change in model fidelity. This study examines how certain obstinate biases in the midlatitude North Atlantic respond to increasing resolution (from 18 to 0.258 in the ocean) and how such biases in sea surface temperature (SST) affect the atmosphere. Using a multimodel ensemble of historical climate simulations run at different horizontal resolutions, it is shown that a severe cold SST bias in the central North Atlantic, common to many ocean models, is significantly reduced with increasing resolution. The associated bias in the time-mean meridional SST gradient is shown to relate to a positive bias in low-level baroclinicity, while the cold SST bias causes biases also in static stability and diabatic heating in the interior of the atmosphere. The changes in baroclinicity and diabatic heating brought by increasing resolution lead to improvements in European blocking and eddy-driven jet variability. Across the multimodel ensemble a clear relationship is found between the climatological meridional SST gradients in the broader Gulf Stream Extension area and two aspects of the atmospheric circulation: the frequency of high-latitude blocking and the southern-jet regime. This relationship is thought to reflect the two-way interaction (with a positive feedback) between the respective oceanic and atmospheric anomalies. These North Atlantic SST anomalies are shown to be important in forcing significant responses in the midlatitude atmospheric circulation, including jet variability and the storm track. Further increases in oceanic and atmospheric resolution are expected to lead to additional improvements in the representation of Euro-Atlantic climate

Repeat Transanal Advancement Flap Repair: Impact on the Overall Healing Rate of High Transsphincteric Fistulas and on Fecal Continence

PURPOSE: Transanal advancement flap repair (TAFR) has been advocated as the treatment of choice for transsphincteric fistulas passing through the upper or middle third of the external anal sphincter. It is not clear whether previous attempts at repair adversely affect the outcome of TAFR. The purpose of the present study was to evaluate the success rate of a repeat TAFR and to assess the impact of such a second procedure on the overall healing rate of high transsphincteric fistulas and on fecal continence. METHODS: Between January 2001 and January 2005, a consecutive series of 87 patients (62 males; median age, 49 (range, 27-73) years) underwent TAFR. Median follow-up was 15 (range, 2-50) months. Patients in whom the initial operation failed were offered two further treatment options: a second flap repair or a long-term indwelling seton drainage. Twenty-six patients (male:female ratio, 5:2; median age, 51 (range, 31-72) years) preferred a repeat repair. Continence status was evaluated before and after the procedures by using the Rockwood Faecal Incontinence Severity Index (RFISI). RESULTS: The healing rate after the first TAFR was 67 percent. Of the 29 patients in whom the initial procedure failed, 26 underwent a repeat TAFR. The healing rate after this second procedure was 69 percent, resulting in an overall success rate of 90 percent. Both before and after the first attempt of TAFR, the median RFISI was 7 (range, 0-34). In patients who underwent a second TAFR, the median RFISI before and after this procedure was 9 (range, 0-34) and 8 (range, 0-34), respectively. None of these changes were statistically significant. CONCLUSIONS: Repeat TAFR increases the overall healing rate of high transsphincteric fistulas from 67 percent after one attempt to 90 percent after two attempts without a deteriorating effect on fecal continence

Impact of resolution on the atmosphere–ocean coupling along the Gulf Stream in global high resolution models

We have investigated the horizontal resolution dependence of the ocean–atmosphere coupling along the Gulf Stream, of simulations made by six Global Climate Models according to the HighResMIP protocol, and compared it with reanalysis and remote sensing observations. Two ocean–atmosphere interaction mechanisms are explored in detail: The Vertical Mixing Mechanism (VMM) associated with the intensification of downward momentum transfer, and the Pressure Adjustment Mechanism (PAM) associated with secondary circulations driven by pressure gradients. Both VMM and PAM are found to be active even in the eddy-parameterized models. However, increasing ocean and/or atmosphere resolution leads to enhanced ocean–atmosphere coupling and improved agreement with reanalysis and observations. Our results indicate that while one part of the stronger air–sea coupling is attributable to the refinement of the oceanic component to eddy-permitting, optimal results are obtained only by further increase of the atmosphere resolution too. The use of the eddy-resolving model show weaker or same coupling strength over the eddy-permitting resolution. We conclude that at least eddy-permiting ocean resolution and comparable atmosphere resolution are required for a reliable ocean–atmosphere coupling along the Gulf Stream

Integrated Modelling Frameworks for Environmental Assessment and Decision Support

As argued in Chapter 1, modern management of environmental resources defines problems from a holistic and integrated perspective, thereby imposing strong requirements on Environmental Decision Support Systems (EDSSs) and Integrated Assessment Tools (IATs). These systems and tools tend to be increasingly complex in terms of software architecture and computational power in order to cope with the type of problems they must solve. For instance, the discipline of Integrated Assessment (IA) needs tools that arc able to span a wide range of disciplines, from socio-economics to ecology to hydrology. Such tools must support a wide range of methodologies and techniques like agent-based modeling, Bayesian decision networks, optimization, multicriteria analyses and visualization tools, to name a few