An Abstraction Theory for Qualitative Models of Biological Systems

Multi-valued network models are an important qualitative modelling approach used widely by the biological community. In this paper we consider developing an abstraction theory for multi-valued network models that allows the state space of a model to be reduced while preserving key properties of the model. This is important as it aids the analysis and comparison of multi-valued networks and in particular, helps address the well-known problem of state space explosion associated with such analysis. We also consider developing techniques for efficiently identifying abstractions and so provide a basis for the automation of this task. We illustrate the theory and techniques developed by investigating the identification of abstractions for two published MVN models of the lysis-lysogeny switch in the bacteriophage lambda.Comment: In Proceedings MeCBIC 2010, arXiv:1011.005

The Discovery of XY Sex Chromosomes in a \u3cem\u3eBoa\u3c/em\u3e and \u3cem\u3ePython\u3c/em\u3e

For over 50 years, biologists have accepted that all extant snakes share the same ZW sex chromosomes derived from a common ancestor [1, 2, 3], with different species exhibiting sex chromosomes at varying stages of differentiation. Accordingly, snakes have been a well-studied model for sex chromosome evolution in animals [1, 4]. A review of the literature, however, reveals no compelling support that boas and pythons possess ZW sex chromosomes [2, 5]. Furthermore, phylogenetic patterns of facultative parthenogenesis in snakes and a sex-linked color mutation in the ball python (Python regius) are best explained by boas and pythons possessing an XY sex chromosome system [6, 7]. Here we demonstrate that a boa (Boa imperator) and python (Python bivittatus) indeed possess XY sex chromosomes, based on the discovery of male-specific genetic markers in both species. We use these markers, along with transcriptomic and genomic data, to identify distinct sex chromosomes in boas and pythons, demonstrating that XY systems evolved independently in each lineage. This discovery highlights the dynamic evolution of vertebrate sex chromosomes and further enhances the value of snakes as a model for studying sex chromosome evolution

Post-Weaning Feed Intake and Performance of Bulls Developed in an Automated Feed Intake Management System

Objective:Our objectives were to compare expected and observed dry matter intake (DMI) and average daily gain (ADG) using modeled nutrient requirement equations, and to evaluate change in DMI over time of beef bull calves fed in an automated feed intake system. Study Description:Feed intake and performance data from purebred Angus, Hereford, and Simmental bull calves across two calf crops [birth years 2021 (n = 40) and 2022 (n = 37)] were utilized for this analysis. Projected DMI and ADG were calculated for each group of bulls by year on an individual basis using the Growing Bull module of the Excel-based Beef Ration and Nutrition Decision Software (BRANDS) formulation program (Iowa State University, Ames, IA). These predicted figures were compared to the Insentec intake data and analyzed via SAS. Results:In 2021–2022, a strong positive correlation (r= 0.78,P\u3c0.01) was observed between actual and predicted DMI. There was a highly correlated (r= 0.84,P\u3c0.01) relationship for the observed and predicted DMI for 2022–2023 as well. Actual ADG for both years was markedly higher than predicted. This result supports that BRANDS more accurately predicts DMI compared to ADG, and that substantial individual intake variation exists. The Bottom Line:DMI increases over time as days of test period increase for growing bulls in an individually fed intake system, and though significant day-to-day variation exists, the BRANDS program appears to more accurately predict DMI than ADG

Effects of Supplementing Corn Silage to Fall-Calving Heifers and Cows Grazing Bermudagrass and Calf Performance and Physiology

The objective was to test the effect of supplemental feeding on cows grazing bermudagrass pastures on cow-calf performance and pasture management. In a completely randomized design, (n = 24) primiparous and multiparous Angus-based cross cows were allocated to bermudagrass pasture with one of two levels of supplemental feeding (non-supplemented or supplemented at 1% of BW on a DM basis of corn silage). Each treatment consisted of (n = 4) pastures stocked with three cows of different ages, a young (first-calf heifer), middle-aged (3-5 yrs.), and old (≥ 6 yrs.) cow, each averaging 155 ± 14 d of gestation at turnout. Cows were fed silage (32-42% DM and 7.83% CP) daily in fence-line bunks, with feeding amount being adjusted at each weigh date. Cows were weighed on 2 consecutive days prior to turnout (middle of the second trimester), midpoint (beginning of the third trimester), and at about 2 weeks prior to the estimated calving date for the herd. Body weight, body condition score, hair score, hair length, and rump fat measurements were taken at each weigh date. Following the final measurement day, cows were relocated to calving pastures consisting of a mixture of bermudagrass, tall fescue, and prairie grass. Supplemental feeding of late gestation fall-calving cows on bermudagrass pasture did not have an effect on cow-calf performance, calf birth weights, and milk output. However, supplemental feeding of cows with corn silage during the summer resulted in 31% more available forage in the pastures. Overall, there were minimal differences in cow performance while grazing bermudagrass pastures during the summer and with supplemental feeding of corn silage. The greatest advantage comes from a greater amount of forage available, which may offset periods of drought or allow producers to increase stocking rates on their property

Effects of Supplementing Corn Silage to Fall-Calving Heifers and Cows Grazing Tall Fescue on Cow Performance

The objective was to test the effect of fescue cultivars and supplemental feeding of cows grazing fescue pastures on cow performance and pasture management. Primiparous and multiparous Angus-based crossed cows (n = 45) averaging 151 ± 7 d of gestation at turnout, were randomly allocated and stratified to pasture treatment by parity. Each pasture contained 3 cows of different ages, consisting of a young (first-calf heifer), middle-aged (3-5 yrs.), and old (≥ 6 yrs.) cow. Treatment was a 2 by 2 factorial design with two types of pasture (toxin producing or non-toxin producing fescue) and two levels of supplemental feeding (non-supplemented or supplemented at 1% of body weight on a DM basis of corn silage). Toxic fescue pastures consisted of K-31 endophyte infected tall fescue (n = 8) tested at 507 ppm ± 0.82 SEM for ergot alkaloids with a 92.5% infection rate. Non-toxic pastures consisted of novel (MaxQ) and endophyte free varieties (n = 7). Cows were fed silage (32-42% DM and 7.83% CP) daily in fence-line bunks, with feeding amount being adjusted at each weigh date. Cows were weighed on 2 consecutive days prior to turnout (middle of the second trimester), midpoint (beginning of the third trimester), and at about 2 weeks prior to the estimated calving date for herd. Body weight, body condition score, hair score, and rump fat measurements were taken at each weigh date. Supplementation tended (P = 0.07) to increase body weight gain and rump fat (P = 0.06) regardless of fescue type. Cattle grazing toxic fescue tended to have longer hair (P = 0.09) and did not “slick” off as quickly as those that were supplemented (P = 0.08). Cattle grazing toxic fescue exhibited classic fescue toxicosis symptoms, and supplementation improved cow performance regardless of fescue cultivar

A Review of Distributions on the String Landscape

We review some basic flux vacua counting techniques and results, focusing on the distributions of properties over different regions of the landscape of string vacua and assessing the phenomenological implications. The topics we discuss include: an overview of how moduli are stabilized and how vacua are counted; the applicability of effective field theory; the uses of and differences between probabilistic and statistical analysis (and the relation to the anthropic principle); the distribution of various parameters on the landscape, including cosmological constant, gauge group rank, and SUSY-breaking scale; "friendly landscapes"; open string moduli; the (in)finiteness of the number of phenomenologically viable vacua; etc. At all points, we attempt to connect this study to the phenomenology of vacua which are experimentally viable.Comment: Invited review, IJMP A. LaTeX. 39 pages. References adde

Processing of Self versus Non-Self in Alzheimer’s Disease

Despite considerable evidence for abnormalities of self-awareness in Alzheimer’s disease (AD), the cognitive mechanisms of altered self-processing in AD have not been fully defined. Here we addressed this issue in a detailed analysis of self/non-self-processing in three patients with AD. We designed a novel neuropsychological battery comprising tests of tactile body schema coding, attribution of tactile events to self versus external agents, and memory for self- versus non-self-generated vocal information, administered in conjunction with a daily life measure of self/non-self-processing (the Interpersonal Reactivity Index). Three male AD patients (aged 54–68 years; one with a pathogenic mutation in the Presenilin 1 gene, one with a pathogenic mutation in the Amyloid Precursor Protein gene, and one with a CSF protein profile supporting underlying AD pathology) were studied in relation to a group of eight healthy older male individuals (aged 58–74 years). Compared to healthy controls, all patients had relatively intact tactile body schema processing. In contrast, all patients showed impaired memory for words previously presented using the patient’s own voice whereas memory for words presented in other voices was less consistently affected. Two patients showed increased levels of emotional contagion and reduced perspective taking on the Interpersonal Reactivity Index. Our findings suggest that AD may be associated with deficient self/non-self differentiation over time despite a relatively intact body image: this profile of altered self-processing contrasts with the deficit of tactile body schema previously described in frontotemporal dementia associated with C9orf72 mutations. We present these findings as a preliminary rationale to direct future systematic study in larger patient cohorts

Extinction filters mediate the global effects of habitat fragmentation on animals

Habitat loss is the primary driver of biodiversity decline worldwide, but the effects of fragmentation (the spatial arrangement of remaining habitat) are debated. We tested the hypothesis that forest fragmentation sensitivity—affected by avoidance of habitat edges—should be driven by historical exposure to, and therefore species’ evolutionary responses to disturbance. Using a database containing 73 datasets collected worldwide (encompassing 4489 animal species), we found that the proportion of fragmentation-sensitive species was nearly three times as high in regions with low rates of historical disturbance compared with regions with high rates of disturbance (i.e., fires, glaciation, hurricanes, and deforestation). These disturbances coincide with a latitudinal gradient in which sensitivity increases sixfold at low versus high latitudes. We conclude that conservation efforts to limit edges created by fragmentation will be most important in the world’s tropical forests

Female-Biased Dispersal and Gene Flow in a Behaviorally Monogamous Mammal, the Large Treeshrew (Tupaia tana)

Background: Female-biased dispersal (FBD) is predicted to occur in monogamous species due to local resource competition among females, but evidence for this association in mammals is scarce. The predicted relationship between FBD and monogamy may also be too simplistic, given that many pair-living mammals exhibit substantial extra-pair paternity. Methodology/Principal Findings: I examined whether dispersal and gene flow are female-biased in the large treeshrew (Tupaia tana) in Borneo, a behaviorally monogamous species with a genetic mating system characterized by high rates (50%) of extra-pair paternity. Genetic analyses provided evidence of FBD in this species. As predicted for FBD, I found lower mean values for the corrected assignment index for adult females than for males using seven microsatellite loci, indicating that female individuals were more likely to be immigrants. Adult female pairs were also less related than adult male pairs. Furthermore, comparison of Bayesian coalescent-based estimates of migration rates using maternally and bi-parentally inherited genetic markers suggested that gene flow is female-biased in T. tana. The effective number of migrants between populations estimated from mitochondrial DNA sequence was three times higher than the number estimated using autosomal microsatellites. Conclusions/Significance: These results provide the first evidence of FBD in a behaviorally monogamous species without mating fidelity. I argue that competition among females for feeding territories creates a sexual asymmetry in the costs an