We introduce a generative model of part‐segmented 3D objects: the shape variational auto‐encoder (ShapeVAE). The ShapeVAE describes a joint distribution over the existence of object parts, the ...locations of a dense set of surface points, and over surface normals associated with these points. Our model makes use of a deep encoder‐decoder architecture that leverages the part‐decomposability of 3D objects to embed high‐dimensional shape representations and sample novel instances. Given an input collection of part‐segmented objects with dense point correspondences the ShapeVAE is capable of synthesizing novel, realistic shapes, and by performing conditional inference enables imputation of missing parts or surface normals. In addition, by generating both points and surface normals, our model allows for the use of powerful surface‐reconstruction methods for mesh synthesis. We provide a quantitative evaluation of the ShapeVAE on shape‐completion and test‐set log‐likelihood tasks and demonstrate that the model performs favourably against strong baselines. We demonstrate qualitatively that the ShapeVAE produces plausible shape samples, and that it captures a semantically meaningful shape‐embedding. In addition we show that the ShapeVAE facilitates mesh reconstruction by sampling consistent surface normals.
Lameness is a severe welfare problem and a production-limiting disease in dairy farming. The objectives of this study were to determine prevalence of lameness and investigate cow- and herd-level ...factors associated with lameness in dairy cows housed in freestall barns in 3 Canadian provinces. A purposive sample of 40 Holstein-Friesian cows was selected from each of 141 dairy farms in Québec, Ontario, and Alberta. In total, 5,637 cows were scored once for lameness (presence of limping when walking). Data collected included information on individual cows (hock lesions, claw length, body condition score, parity, days in milk, and milk production), management practices (floor and stall cleaning routine, bedding routine, and footbath practices), and facility design (stall dimensions, stall base and bedding type, width of feed alley, flooring type, and slipperiness) hypothesized to be risk factors for lameness. Multilevel mixed logistic regression models were constructed (including farm as a random effect and province as a fixed effect). Herd-level lameness prevalence ranged from 0 to 69% (mean=21%). Lameness prevalence increased with increasing parity; compared with first parity, cows in parity 2, 3, and ≥4 had 1.6, 3.3, and 4 times, respectively, higher odds of being lame. Furthermore, the odds of lameness were 1.6 times greater in cows with low body condition score (≤2.5) than in cows with a higher body condition score. In addition, injured hocks and overgrown claws were associated with 1.4- and 1.7-fold increased odds of being lame, respectively, whereas every 1kg increase in daily milk production was associated with a 3% decrease in the odds of being lame. Lameness prevalence was higher in herds with ≤100 cows, but lower in barns with a sand or dirt stall base, or with bedding ≥2cm deep. Cows exposed to very slippery floors had 2 times the odds of being lame compared with cows exposed to nonslippery floors. We attributed the wide range of lameness prevalence to the great variability in facilities and management practices among farms. Finally, we inferred that the prevalence of lameness could be decreased by improving management of multiparous, thin, or injured cows and by adopting management practices intended to improve cow comfort, namely the floor’s slip resistance and the stall’s lying surface.
R (R Core Team 2014) provides a powerful and flexible system for statistical computations. It has a default-install set of functionality that can be expanded by the use of several thousand add-in ...packages as well as user-written scripts. While R is itself a programming language, it has proven relatively easy to incorporate programs in other languages, particularly Fortran and C. Success, however, can lead to its own costs: • Users face a confusion of choice when trying to select packages in approaching a problem. • A need to maintain workable examples using early methods may mean some tools offered as a default may be dated. • In an open-source project like R, how to decide what tools offer "best practice" choices, and how to implement such a policy, present a serious challenge. We discuss these issues with reference to the tools in R for nonlinear parameter estimation (NLPE) and optimization, though for the present article `optimization` will be limited to function minimization of essentially smooth functions with at most bounds constraints on the parameters. We will abbreviate this class of problems as NLPE. We believe that the concepts proposed are transferable to other classes of problems seen by R users.
Lying behavior is an important measure of comfort and well-being in dairy cattle, and changes in lying behavior are potential indicators and predictors of lameness. Our objectives were to determine ...individual and herd-level risk factors associated with measures of lying behavior, and to evaluate whether automated measures of lying behavior can be used to detect lameness. A purposive sample of 40 Holstein cows was selected from each of 141 dairy farms in Alberta, Ontario, and Québec. Lying behavior of 5,135 cows between 10 and 120 d in milk was automatically and continuously recorded using accelerometers over 4 d. Data on factors hypothesized to influence lying behavior were collected, including information on individual cows, management practices, and facility design. Associations between predictor variables and measures of lying behavior were assessed using generalized linear mixed models, including farm and province as random and fixed effects, respectively. Logistic regression models were used to determine whether lying behavior was associated with lameness. At the cow-level, daily lying time increased with increasing days in milk, but this effect interacted with parity; primiparous cows had more frequent but shorter lying bouts in early lactation, changing to mature-cow patterns of lying behavior (fewer and longer lying bouts) in late lactation. In barns with stall curbs >22cm high, the use of sand or >2cm of bedding was associated with an increased average daily lying time of 1.44 and 0.06h/d, respectively. Feed alleys ≥350cm wide or stalls ≥114cm wide were associated with increased daily lying time of 0.39 and 0.33h/d, respectively, whereas rubber flooring in the feed alley was associated with 0.47h/d lower average lying time. Lame cows had longer lying times, with fewer, longer, and more variable duration of bouts compared with nonlame cows. In that regard, cows with lying time ≥14h/d, ≤5 lying bouts per day, bout duration ≥110min/bout, or standard deviations of bout duration over 4 d ≥70min had 3.7, 1.7, 2.5, and 3.0higher odds of being lame, respectively. Factors related to comfort of lying and standing surfaces significantly affected lying behavior. Finally, we inferred that automated measures of lying behavior could contribute to lameness detection, especially when interpreted in the context of other factors known to affect lying behavior, including those associated with the individual cow (e.g., parity and stage of lactation) or environment (e.g., stall surface).
Coralline algae are key biological substrates of many carbonate systems globally. Their capacity to build enduring crusts that underpin the formation of tropical reefs, rhodolith beds and other ...benthic substrate is dependent on the formation of a calcified thallus. However, this important process of skeletal carbonate formation is not well understood. We undertook a study of cellular carbonate features to develop a model for calcification. We describe two types of cell wall calcification; 1) calcified primary cell wall (PCW) in the thin-walled elongate cells such as central medullary cells in articulated corallines and hypothallial cells in crustose coralline algae (CCA), 2) calcified secondary cell wall (SCW) with radial Mg-calcite crystals in thicker-walled rounded cortical cells of articulated corallines and perithallial cells of CCA. The distinctive banding found in many rhodoliths is the regular transition from PCW-only cells to SCW cells. Within the cell walls there can be bands of elevated Mg with Mg content of a few mol% higher than radial Mg-calcite (M-type), ranging up to dolomite composition (D-type).
We propose the following three-step model for calcification. 1) A thin (< 0.5 μm) PCW forms and is filled with a mineralising fluid of organic compounds and seawater. Nanometer-scale Mg-calcite grains precipitate on the organic structures within the PCW. 2) Crystalline cellulose microfibrils (CMF) are extruded perpendicularly from the cellulose synthase complexes (CSC) in the plasmalemma to form the SCW. 3) The CMF soaks in the mineralising fluid as it extrudes and becomes calcified, retaining the perpendicular form, thus building the radial calcite. In Clathromorphum, SCW formation lags PCW creating a zone of weakness resulting in a split in the sub-surface crust. All calcification seems likely to be a bioinduced rather than controlled process. These findings are a substantial step forward in understanding how corallines calcify.
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Nonlinear Parameter Optimization Using R John C. Nash, Telfer School of Management, University of Ottawa, Canada A systematic and comprehensive treatment of optimization software using R In recent ...decades, optimization techniques have been streamlined by computational and artificial intelligence methods to analyze more variables, especially under non–linear, multivariable conditions, more quickly than ever before. Optimization is an important tool for decision science and for the analysis of physical systems used in engineering. Nonlinear Parameter Optimization with R explores the principal tools available in R for function minimization, optimization, and nonlinear parameter determination and features numerous examples throughout. Nonlinear Parameter Optimization with R: * Provides a comprehensive treatment of optimization techniques * Examines optimization problems that arise in statistics and how to solve them using R * Enables researchers and practitioners to solve parameter determination problems * Presents traditional methods as well as recent developments in R * Is supported by an accompanying website featuring R code, examples and datasets Researchers and practitioners who have to solve parameter determination problems who are users of R but are novices in the field optimization or function minimization will benefit from this book. It will also be useful for scientists building and estimating nonlinear models in various fields such as hydrology, sports forecasting, ecology, chemical engineering, pharmaco- kinetics, agriculture, economics and statistics.
Cow comfort in tiestalls is directly affected by stall dimensions, for which some recommendations exist. To evaluate how well Canadian dairy farms with tiestalls complied with recommendations for ...stall dimensions, as well as the effect of compliance on cow comfort and cleanliness, we assessed lactating Holstein cows (n = 3,485) on 100 tiestall dairy farms for neck and leg lesions, lameness, and cleanliness and measured time spent lying down. Data on stall dimensions (width and length of the stall, position and height of the tie rail, length of the chain, and height of the manger curb) were recorded for each cow. The majority of cows were housed in stalls smaller than recommended. The prevalence of lesions and lameness was high (neck, 33%; knee, 44%; hock; 58%, lameness, 25%) and the prevalence of dirtiness was low (udder, 4%; flank, 11%; legs, 4%). Chains shorter than recommended increased the risk of neck, knee, and hock lesions. A tie rail further back in the stall than recommended increased the risk of neck, knee, and hock lesions and reduced the frequency of lying bouts and the risk of a dirty udder. A tie rail set lower than recommended decreased the risk of neck lesions and lameness and increased lying time and lying bout frequency. Stalls narrower in width than recommended increased the risk of neck injuries and lameness and reduced the daily duration of lying time and the risk of a dirty flank and legs. Stalls shorter in length than recommended increased the risk of knee lesions and reduced lying bout frequency and the risk of a dirty udder. The majority of farms do not follow recommendations for stall dimensions (with the exception of tie rail height), and the lack of compliance is associated with increased risk of lesions and lameness and can affect lying time. Recommended stall dimensions tend to reduce cleanliness, but the prevalence of dirty cows remains very low.
R users can often solve optimization tasks easily using the tools in the optim function in the stats package provided by default on R installations. However, there are many other optimization and ...nonlinear modelling tools in R or in easily installed add-on packages. These present users with a bewildering array of choices. optimx is a wrapper to consolidate many of these choices for the optimization of functions that are mostly smooth with parameters at most bounds-constrained. We attempt to provide some diagnostic information about the function, its scaling and parameter bounds, and the solution characteristics. optimx runs a battery of methods on a given problem, thus facilitating comparative studies of optimization algorithms for the problem at hand. optimx can also be a useful pedagogical tool for demonstrating the strengths and pitfalls of different classes of optimization approaches including Newton, gradient, and derivative-free methods.
. Wet chemical analysis of solid as affected by molar ratio and pH (normalized ion ratio in precipitates PO
4
=
1).
Display omitted
▶ A hybrid process was efficient to remove phosphate and fluoride ...from wastewater. ▶ Optimum pH and molar ratio, (Ca
+2: PO
4
3−: F
−), were determined. ▶ Both precipitates and filtrate could potentially be reused.
The removal of phosphate and fluoride from thin-film transistor liquid crystal display (TFT-LCD) wastewater by a hybrid precipitation–microfiltration (MF) process was studied. Calcium salt was used to form precipitates, followed by crossflow MF for solid–liquid separation. The results showed that excess calcium could induce effective removal of phosphate and fluoride at pH 8.5 and 10.5. The dominant solids were hydroxyapatite (Ca
5(PO
4)
3OH, HAP), amorphous calcium phosphate (ACP), fluorapatite (Ca
5(PO
4)
3F, FAP), and calcium fluoride (CaF
2). Precipitation conditions affected the MF, and more significant fouling was found at pH 8.5 than pH 10.5. Permeate analysis showed increased removal of phosphate and fluoride in MF, and effective removal of turbidity. The initial flux and steady state flux increased with increasing filtration pressure and crossflow velocity. The main fouling resistance was cake resistance. This study demonstrated that the hybrid precipitation–MF process could effectively remove phosphate and fluoride from wastewater, and produce filtrate and precipitates for potential recovery and reuse.
Reflects on what new understandings can be gained from developing a new theoretical vocabulary of performance, and explores the imaginative and material geographies of cultural performativity and ...embodiment. Considers what is to be gained from the metaphorical and substantive turn from 'text' and representations, to performance and practices. Focuses particularly on dance.
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