Management, feeding, production, reproduction and udder health on organic and conventional Swiss dairy farms

Organic dairy farms (OP; n=60) and conventional dairy farms (integrated production, IP; n=60), matched in size, location, and agricultural zone (altitude), were studied for possible differences in management, feeding, production, reproduction and udder health. OP and IP farms were similar in size (17.7 and 16.9 ha), milk quota (65900 and 70,000 kg/year), cow number (14 and 15), cow age (5.3 and 5.2 years), housing of cows of the Simmental x Red Holstein or Holstein breeds (87 and 75%; 45 and 60%), but differed significantly with respect to loose housing systems (18 and 7%), outside paddocks (98 and 75%), energy-corrected 305-d milk yield (5,695 and 6,059 kg), milk protein content (31.8 and 32.7 g/kg), use of bucket milking systems (73 and 33%), observance of regular (12-h) milking intervals (47 and 68%), routine application of the California-Mastitis-Test (10 and 28%), teat dipping after milking (25 and 43%) and blanket dry cow treatments (0 and 45%). Milk somatic cell counts on OP and IP farms (119 000 and 117,000/mL) and reproduction data were similar and there were no significant differences between OP and IP farms as concerns available feeds, planning and management of feeding. Alternative veterinary treatments were used more often on OP than IP farms (55 and 17%). Main causes for cow replacements on OP and IP farms were fertility disorders (both 45%), age (40 and 42%), sale (30 and 37%) and udder health (35 and 13%).Between OP and IP Swiss dairy farms thus relatively few larger differences were found.

Evaluation of late results in breast reconstruction by latissimus dorsi flap and prosthesis implantation

BACKGROUND: Breast reconstruction by latissimus dorsi myocutaneous flap in combination with a prosthesis is a widely used, well-established procedure. Short- and medium-term evaluation after this procedure is well described in the literature, but there have been no evaluations of the late course (over 10 years) published until now. METHODS: In a retrospective study, 68 patients operated on by means of this technique at the authors' institution from 1981 to 1993 resulting in a minimal follow-up of 10 years were included. Patients were invited to an interrogation, clinical examination, and photographic documentation (n = 51). Incidence of late flap or prosthesis-related complications, number of and indications for corrective procedures, and the correlation of the patients' subjective judgment and objective results in the late course have been the main interest of the authors' survey. RESULTS: The authors found that 50 percent of the patients needed a late reoperation for change or removal of the prosthesis. Seven (10 percent) of 68 patients needed a definitive removal of the implant in the late course. Assessment of the photographic documentation of the late result by four nonprofessionals showed that the objective aesthetic results of a considerable number of the authors' reconstructions were not sufficient. CONCLUSION: The procedure combines two basic techniques of reconstructive surgery, the soft-tissue restoration by a pedicled flap as the autologous reconstructive component and the volume reconstruction by prosthesis. Therefore, these patients are subject to a cumulation of the basic morbidity of the two techniques. The authors conclude that the indication for this procedure should be restricted to patients not qualifying for "pure" reconstructive techniques.

Detection of exon deletions within an entire gene (CFTR) by relative quantification on the LightCycler

BACKGROUND: Cystic fibrosis (CF) is associated with at least 1 pathogen point sequence variant on each CFTR allele. Some symptomatic patients, however, have only 1 detectable pathogen sequence variant and carry, on the other allele, a large deletion that is not detected by conventional screening methods. METHODS: For relative quantitative real-time PCR detection of large deletions in the CFTR gene, we designed DNA-specific primers for each exon of the gene and primers for a reference gene (beta2-microglobulin). For PCR we used a LightCycler system (Roche) and calculated the gene-dosage ratio of CFTR to beta2-microglobulin. We tested the method by screening all 27 exons in 3 healthy individuals and 2 patients with only 1 pathogen sequence variant. We then performed specific deletion screenings in 10 CF patients with known large deletions and a blinded analysis in which we screened 24 individuals for large deletions by testing 8 of 27 exons. RESULTS: None of the ratios for control samples were false positive (for deletions or duplications); moreover, for all samples from patients with known large deletions, the calculated ratios for deleted exons were close to 0.5. In addition, the results from the blinded analysis demonstrated that our method can also be used for the screening of single individuals. CONCLUSIONS: The LightCycler assay allows reliable and rapid screening for large deletions in the CFTR gene and detects the copy number of all 27 exons.

A Faster Circular Binary Segmentation Algorithm for the Analysis of Array CGH Data

Motivation: Array CGH technologies enable the simultaneous measurement of DNA copy number for thousands of sites on a genome. We developed the circular binary segmentation (CBS) algorithm to divide the genome into regions of equal copy number (Olshen {\it et~al}, 2004). The algorithm tests for change-points using a maximal $t$-statistic with a permutation reference distribution to obtain the corresponding $p$-value. The number of computations required for the maximal test statistic is $O(N^2),$ where $N$ is the number of markers. This makes the full permutation approach computationally prohibitive for the newer arrays that contain tens of thousands markers and highlights the need for a faster. algorithm. Results: We present a hybrid approach to obtain the $p$-value of the test statistic in linear time. We also introduce a rule for stopping early when there is strong evidence for the presence of a change. We show through simulations that the hybrid approach provides a substantial gain in speed with only a negligible loss in accuracy and that the stopping rule further increases speed. We also present the analysis of array CGH data from a breast cancer cell line to show the impact of the new approaches on the analysis of real data. Availability: An R (R Development Core Team, 2006) version of the CBS algorithm has been implemented in the ``DNAcopy'' package of the Bioconductor project (Gentleman {\it et~al}, 2004). The proposed hybrid method for the $p$-value is available in version 1.2.1 or higher and the stopping rule for declaring a change early is available in version 1.5.1 or higher.

Chronic excessive erythrocytosis induces endothelial activation and damage in mouse brain

Excessive erythrocytosis results in severely increased blood viscosity, which may have significant detrimental effects on endothelial cells and, ultimately, function of the vascular endothelium. Because blood-brain barrier stability is crucial for normal physiological function, we used our previously characterized erythropoietin-overexpressing transgenic (tg6) mouse line (which has a hematocrit of 0.8-0.9) to investigate the effect of excessive erythrocytosis on vessel number, structure, and integrity in vivo. These mice have abnormally high levels of nitric oxide (NO), a potent proinflammatory molecule, suggesting altered vascular permeability and function. In this study, we observed that brain vessel density of tg6 mice was significantly reduced (16%) and vessel diameter was significantly increased (15%) compared with wild-type mice. Although no significant increases in vascular permeability under normoxic or acute hypoxic conditions (8% O2 for 4 h) were detected, electron-microscopic analysis revealed altered morphological characteristics of the tg6 endothelium. Tg6 brain vascular endothelial cells appeared to be activated, with increased luminal protrusions reminiscent of ongoing inflammatory processes. Consistent with this observation, we detected increased levels of intercellular adhesion molecule-1 and von Willebrand factor, markers of endothelial activation and damage, in brain tissue. We propose that chronic excessive erythrocytosis and sustained high hematocrit cause endothelial damage, which may, ultimately, increase susceptibility to vascular disease.

Bayesian Hidden Markov Modeling of Array CGH Data

Genomic alterations have been linked to the development and progression of cancer. The technique of Comparative Genomic Hybridization (CGH) yields data consisting of fluorescence intensity ratios of test and reference DNA samples. The intensity ratios provide information about the number of copies in DNA. Practical issues such as the contamination of tumor cells in tissue specimens and normalization errors necessitate the use of statistics for learning about the genomic alterations from array-CGH data. As increasing amounts of array CGH data become available, there is a growing need for automated algorithms for characterizing genomic profiles. Specifically, there is a need for algorithms that can identify gains and losses in the number of copies based on statistical considerations, rather than merely detect trends in the data. We adopt a Bayesian approach, relying on the hidden Markov model to account for the inherent dependence in the intensity ratios. Posterior inferences are made about gains and losses in copy number. Localized amplifications (associated with oncogene mutations) and deletions (associated with mutations of tumor suppressors) are identified using posterior probabilities. Global trends such as extended regions of altered copy number are detected. Since the posterior distribution is analytically intractable, we implement a Metropolis-within-Gibbs algorithm for efficient simulation-based inference. Publicly available data on pancreatic adenocarcinoma, glioblastoma multiforme and breast cancer are analyzed, and comparisons are made with some widely-used algorithms to illustrate the reliability and success of the technique.

rs1004819 is the main disease-associated IL23R variant in German Crohn's disease patients: combined analysis of IL23R, CARD15, and OCTN1/2 variants

BACKGROUND: The IL23R gene has been identified as a susceptibility gene for inflammatory bowel disease (IBD) in the North American population. The aim of our study was to test this association in a large German IBD cohort and to elucidate potential interactions with other IBD genes as well as phenotypic consequences of IL23R variants. METHODS: Genomic DNA from 2670 Caucasian individuals including 833 patients with Crohn's disease (CD), 456 patients with ulcerative colitis (UC), and 1381 healthy unrelated controls was analyzed for 10 IL23R SNPs. Genotyping included the NOD2 variants p.Arg702Trp, p.Gly908Arg, and p.Leu1007fsX1008 and polymorphisms in SLC22A4/OCTN1 (1672 C-->T) and SLC22A5/OCTN2 (-207 G-->C). RESULTS: All IL23R gene variants analyzed displayed highly significant associations with CD. The strongest association was found for the SNP rs1004819 [P = 1.92x10(-11); OR 1.56; 95 % CI (1.37-1.78)]. 93.2% of the rs1004819 TT homozygous carriers as compared to 78% of CC wildtype carriers had ileal involvement [P = 0.004; OR 4.24; CI (1.46-12.34)]. The coding SNP rs11209026 (p.Arg381Gln) was protective for CD [P = 8.04x10(-8); OR 0.43; CI (0.31-0.59)]. Similar, but weaker associations were found in UC. There was no evidence for epistasis between the IL23R gene and the CD susceptibility genes CARD15 and SLC22A4/5. CONCLUSION: IL23R is an IBD susceptibility gene, but has no epistatic interaction with CARD15 and SLC22A4/5. rs1004819 is the major IL23R variant associated with CD in the German population, while the p.Arg381Gln IL23R variant is a protective marker for CD and UC.

Fatal adenovirus hepatitis during maintenance therapy for childhood acute lymphoblastic leukemia

Disseminated adenoviral infection with hepatitis is rare in children undergoing standard chemotherapy. We report on a 3(1/2)-year-old male with fatal adenovirus hepatitis receiving maintenance chemotherapy for acute lymphoblastic leukemia (ALL). Adenoviral hepatitis was proven by histology, viral culture, and PCR in a liver biopsy. Quantitative real-time PCR in the peripheral blood showed adenoviral DNA copy number >10(9)/ml. Despite aggressive supportive care and antiviral treatment with cidofovir, the patient died rapidly due to fulminant liver failure. Diagnostic and treatment options for adenovirus infection remain unsatisfactory for these patients. We propose suggestions for diagnosis and therapy.

Paleoenvironmental reconstructions from cave sediments of the Moravian Karst, Czech Republic / by Pavel Sroubek.

This thesis presents a paleoclimatic/paleoenvironmental study conducted on clastic cave sediments of the Moravian Karst, Czech Republic. The study is based on environmental magnetic techniques, yet a wide range of other scientific methods was used to obtain a clearer picture of the Quaternary climate. My thesis also presents an overview of the significance of cave deposits for paleoclimatic reconstructions, explains basic environmental magnetic techniques and offers background information on the study area – a famous karst region in Central Europe with a rich history. In Kulna Cave magnetic susceptibility variations and in particular variations in pedogenic susceptibility yield a detailed record of the palaeoenvironmental conditions during the Last Glacial Stage. The Kulna long-term climatic trends agree with the deep-sea SPECMAP record, while the short-term oscillations correlate with rapid changes in the North Atlantic sea surface temperatures. Kulna Cave sediments reflect the intensity of pedogenesis controlled by short-term warmer events and precipitation over the mid-continent and provide a link between continental European climate and sea surface temperatures in the North Atlantic during the Last Glacial Stage. Given the number of independent climate proxies determined from the entrance facies of the cave and their high resolution, Kulna is an extremely important site for studying Late Pleistocene climate. In the interior of Spiralka Cave, a five meter high section of fine grained sediments deposited during floods yields information on the climatic and environmental conditions of the last millenium. In the upper 1.5 meters of this profile, mineral magnetic and other non-magnetic data indicate that susceptibility variations are controlled by the concentration of magnetite and its magnetic grain size. Comparison of our susceptibility record to the instrumental record of winter temperature anomalies shows a remarkable correlation. This correlation is explained by coupling of the flooding events, cultivation of land and pedogenetic processes in the cave catchment area. A combination of mineral magnetic and geochemical proxies yields a detail picture of the rapidly evolving climate of the near past and tracks both natural and human induced environmental changes taking place in the broader region.

High cycle fatigue of AA6082 and AA6063 aluminum extrusions

The high cycle fatigue behavior of hollow extruded AA6082 and AA6063 aluminum extrusions has been studied. Hollow extruded aluminum profiles can be processed into intricate shapes, and may be suitable replacements for fatigue critical automotive applications requiring reduced weight. There are several features inherent in hollow aluminum extrusions, such as seam welds, charge welds, microstructural variations and die lines. The effects of such extrusion variables on high cycle fatigue properties were studied by taking specimens from an actual car bumper extrusion. It appears that extrusion die lines create large anisotropy differences in fatigue properties, while welds themselves have little effect on fatigue lives. Removal of die lines greatly increased fatigue properties of AA6082 specimens taken transverse to the extrusion direction. Without die lines, anisotropy in fatigue properties between AA6082 specimens taken longitudinal and transverse to the extrusion direction, was significantly reduced, and properties associated with the orientation of the microstructure appears to be isotropic. A fibrous microstructure for AA6082 specimens showed great improvements in fatigue behavior. The effects of elevated temperatures and exposure of specimens to NaCl solutions was also studied. Exposure to the salt solution greatly reduced the fatigue lives of specimens, while elevated temperatures showed more moderate reductions in fatigue lives.

RISK OF SHUNT-DEPENDENT HYDROCEPHALUS AFTER OCCLUSION OF RUPTURED INTRACRANIAL ANEURYSMS BY SURGICAL CLIPPING OR ENDOVASCULAR COILING: A SINGLE-INSTITUTION SERIES AND META-ANALYSIS

OBJECTIVE: To compare the risk of shunt-dependent hydrocephalus after treatment of ruptured intracranial aneurysms by clipping versus coiling. METHODS: We analyzed 596 patients prospectively added to our database from July of 1999 to November of 2005 concerning the risk of shunt dependency after clipping versus coiling. Factors analyzed included age; sex; Hunt and Hess grade; Fisher grade; acute hydrocephalus; intraventricular hemorrhage; angiographic vasospasm; and number, size, and location of aneurysms. In addition, a meta-analysis of available data from the literature was performed identifying four studies with quantitative data on the frequency of clip, coil, and shunt dependency. RESULTS: The institutional series revealed Hunt and Hess grade, Fisher grade, acute hydrocephalus, intraventricular hemorrhage, and angiographic vasospasm as significant (P < 0.05) risk factors for shunt dependency after a univariate analysis. In a multivariate logistic regression analysis, we isolated intraventricular hemorrhage, acute hydrocephalus, and angiographic vasospasm as independent, significant risk factors for shunt dependency. The meta-analysis, including the current data, revealed a significantly higher risk for shunt dependency after coiling than after clipping (P = 0.01). CONCLUSION: Clipping of a ruptured aneurysm may be associated with a lower risk for developing shunt dependency, possibly by clot removal. This might influence long-term outcome and surgical decision making.

Development of an optimization model for biofuel facility size and location and a simulation model for design of a biofuel supply chain

To mitigate greenhouse gas (GHG) emissions and reduce U.S. dependence on imported oil, the United States (U.S.) is pursuing several options to create biofuels from renewable woody biomass (hereafter referred to as “biomass”). Because of the distributed nature of biomass feedstock, the cost and complexity of biomass recovery operations has significant challenges that hinder increased biomass utilization for energy production. To facilitate the exploration of a wide variety of conditions that promise profitable biomass utilization and tapping unused forest residues, it is proposed to develop biofuel supply chain models based on optimization and simulation approaches. The biofuel supply chain is structured around four components: biofuel facility locations and sizes, biomass harvesting/forwarding, transportation, and storage. A Geographic Information System (GIS) based approach is proposed as a first step for selecting potential facility locations for biofuel production from forest biomass based on a set of evaluation criteria, such as accessibility to biomass, railway/road transportation network, water body and workforce. The development of optimization and simulation models is also proposed. The results of the models will be used to determine (1) the number, location, and size of the biofuel facilities, and (2) the amounts of biomass to be transported between the harvesting areas and the biofuel facilities over a 20-year timeframe. The multi-criteria objective is to minimize the weighted sum of the delivered feedstock cost, energy consumption, and GHG emissions simultaneously. Finally, a series of sensitivity analyses will be conducted to identify the sensitivity of the decisions, such as the optimal site selected for the biofuel facility, to changes in influential parameters, such as biomass availability and transportation fuel price. Intellectual Merit The proposed research will facilitate the exploration of a wide variety of conditions that promise profitable biomass utilization in the renewable biofuel industry. The GIS-based facility location analysis considers a series of factors which have not been considered simultaneously in previous research. Location analysis is critical to the financial success of producing biofuel. The modeling of woody biomass supply chains using both optimization and simulation, combing with the GIS-based approach as a precursor, have not been done to date. The optimization and simulation models can help to ensure the economic and environmental viability and sustainability of the entire biofuel supply chain at both the strategic design level and the operational planning level. Broader Impacts The proposed models for biorefineries can be applied to other types of manufacturing or processing operations using biomass. This is because the biomass feedstock supply chain is similar, if not the same, for biorefineries, biomass fired or co-fired power plants, or torrefaction/pelletization operations. Additionally, the research results of this research will continue to be disseminated internationally through publications in journals, such as Biomass and Bioenergy, and Renewable Energy, and presentations at conferences, such as the 2011 Industrial Engineering Research Conference. For example, part of the research work related to biofuel facility identification has been published: Zhang, Johnson and Sutherland [2011] (see Appendix A). There will also be opportunities for the Michigan Tech campus community to learn about the research through the Sustainable Future Institute.

In-situ measurement and characterization of cloud particles using digital in-line holography

Satellite measurement validations, climate models, atmospheric radiative transfer models and cloud models, all depend on accurate measurements of cloud particle size distributions, number densities, spatial distributions, and other parameters relevant to cloud microphysical processes. And many airborne instruments designed to measure size distributions and concentrations of cloud particles have large uncertainties in measuring number densities and size distributions of small ice crystals. HOLODEC (Holographic Detector for Clouds) is a new instrument that does not have many of these uncertainties and makes possible measurements that other probes have never made. The advantages of HOLODEC are inherent to the holographic method. In this dissertation, I describe HOLODEC, its in-situ measurements of cloud particles, and the results of its test flights. I present a hologram reconstruction algorithm that has a sample spacing that does not vary with reconstruction distance. This reconstruction algorithm accurately reconstructs the field to all distances inside a typical holographic measurement volume as proven by comparison with analytical solutions to the Huygens-Fresnel diffraction integral. It is fast to compute, and has diffraction limited resolution. Further, described herein is an algorithm that can find the position along the optical axis of small particles as well as large complex-shaped particles. I explain an implementation of these algorithms that is an efficient, robust, automated program that allows us to process holograms on a computer cluster in a reasonable time. I show size distributions and number densities of cloud particles, and show that they are within the uncertainty of independent measurements made with another measurement method. The feasibility of another cloud particle instrument that has advantages over new standard instruments is proven. These advantages include a unique ability to detect shattered particles using three-dimensional positions, and a sample volume size that does not vary with particle size or airspeed. It also is able to yield two-dimensional particle profiles using the same measurements.

Problems in the classical calculus of variations

This dissertation concerns convergence analysis for nonparametric problems in the calculus of variations and sufficient conditions for weak local minimizer of a functional for both nonparametric and parametric problems. Newton's method in infinite-dimensional space is proved to be well-defined and converges quadratically to a weak local minimizer of a functional subject to certain boundary conditions. Sufficient conditions for global converges are proposed and a well-defined algorithm based on those conditions is presented and proved to converge. Finite element discretization is employed to achieve an implementable line-search-based quasi-Newton algorithm and a proof of convergence of the discretization of the algorithm is included. This work also proposes sufficient conditions for weak local minimizer without using the language of conjugate points. The form of new conditions is consistent with the ones in finite-dimensional case. It is believed that the new form of sufficient conditions will lead to simpler approaches to verify an extremal as local minimizer for well-known problems in calculus of variations.

Enhancement of heterologous expression of alkaline phytase in Pichia pastors

Phytic acid is the major storage form of phosphorus and inositol in seeds and legumes. It forms insoluble phytate salts by chelating with positively charged mineral ions. Non-ruminant animals are not able to digest phytate due to the lack of phytases in their GI tracks, thus the undigested phytate is excreted leading to environmental contamination. Supplementation with phytases in animal feed has proven to be an effective strategy to alleviate nutritional and environmental issues. The unique catalytic and thermal stability properties of alkaline phytase from lily pollen (LlALP) suggest that it has the potential to be useful as a feed supplement. Our goal is to develop a method for the production of substantial amounts of rLlALP for animal feed and structural studies. rLlALP2 has been successfully expressed in the yeast, Pichia pastoris. However, expression yield was modest (8-10 mg/L). Gene copy number has been identified as an important parameter in enhancing protein yields. Multicopy clones were selected using Zeocin-resistance-based vectors and challenging transformants to high Zeocin levels under different conditions. Data indicate that increasing selection pressure led to the generation of clones with amplification of both rLlAlp2 and Zeor genes and the two genes were not equally amplified. Additionally, clones generated by step-wise methods led to clones with greater amplification. The effects of transgene copy number and gene sequence optimization on expression levels of rLlALP2 were examined. The data indicate that increasing the copy number of rLlAlp2 in transformed clones was detrimental to expression level. The use of a sequence-optimized rLlAlp2 (op-rLlAlp2) increased expression yield of the active enzyme by 25-50%, suggesting that transcription and translation efficiency are not major bottlenecks in the production of rLlALP2. Lowering induction temperature to 20 oC led to an increase in enzyme activity of 1.2 to 20-fold, suggesting that protein folding or post-translational processes may be limiting factors for rLlALP2 production. Cumulatively, optimization of copy number, gene sequence optimization and reduced temperature led to increase of rLlALP2 enzyme activity by three-fold (25-30 mg/L). In an effort to simplify the purification process of rLlALP2, extracellular expression of phytase was investigated. Extracellular expression is dependent on the presence of an appropriate secretion signal upstream of the transgene native signal peptide(s) present in the transgene may also influence secretion efficiency. The data suggest that deletion of both N- and C-terminal signal peptides of rLlALP2 enhanced α-mating factor (α-MF)-driven secretion of LlALP2 by four-fold. The secretion signal peptide of chicken egg white lysozyme was ineffective in secretion rLlALP2 in P. pastoris. To enhance rLlALP2 secretion, effectiveness of the strong inducible promoter (PAOX1) was compared with the constitutive promoter (PGAP). The intracellular yield of rLlALP2 was about four-fold greater under the control of PGAP compared to PAOX1 and extracellular expression level of rLlALP2 was around eight-fold (75-100 mg/L) greater. The successful production of active rLlALP2 in P. pastoris will allow us to conduct the animal feed supplementation studies and structural studies.