Miracle-dz/UniFAR-FTUs huggingface dataset:
Statistical Applications in Genetics and Molecular Biology Fitting Boolean Networks from Steady State Perturbation Data

Gene perturbation experiments are commonly used for the reconstruction of gene regulatory networks. Typical experimental methodology imposes persistent changes on the network. The resulting data must therefore be interpreted as a steady state from an altered gene regulatory network, rather than a direct observation of the original network. In this article an implicit modeling methodology is proposed in which the unperturbed network of interest is scored by first modeling the persistent perturbation, then predicting the steady state, which may then be compared to the observed data. This results in a many-to-one inverse problem, so a computational Bayesian approach is used to assess model uncertainty. The methodology is first demonstrated on a number of synthetic networks. It is shown that the Bayesian approach correctly assigns high posterior probability to the network structure and steady state behavior. Further, it is demonstrated that where uncertainty of model features is indicated, the uncertainty may be accurately resolved with further perturbation experiments. The methodology is then applied to the modeling of a gene regulatory network using perturbation data from nine genes which have been shown to respond synergistically to known oncogenic mutations. A hypothetical model emerges which conforms to reported regulatory properties of these genes. Furthermore, the Bayesian methodology is shown to be consistent in the sense that multiple randomized applications of the fitting algorithm converge to an approximately common posterior density on the space of models. Such consistency is generally not feasible for algorithms which report only single models. We conclude that fully Bayesian methods, coupled with models which accurately account for experimental constraints, are a suitable tool for the inference of gene regulatory networks, in terms of accuracy, estimation of model uncertainty, and experimental design.
Statistical Applications in Genetics and Molecular Biology Large-scale Parentage Inference with SNPs : an Efficient Algorithm for Statistical Confidence of Parent Pair Allocations

Advances in genotyping that allow tens of thousands of individuals to be genotyped at a moderate number of single nucleotide polymorphisms (SNPs) permit parentage inference to be pursued on a very large scale. The intergenerational tagging this capacity allows is revolutionizing the management of cultured organisms (cows, salmon, etc.) and is poised to do the same for scientific studies of natural populations. Currently, however, there are no likelihood-based methods of parentage inference which are implemented in a manner that allows them to quickly handle a very large number of potential parents or parent pairs. Here we introduce an efficient likelihoodbased method applicable to the specialized case of cultured organisms in which both parents can be reliably sampled. We develop a Markov chain representation for the cumulative number of Mendelian incompatibilities between an offspring and its putative parents and we exploit it to develop a fast algorithm for simulation-based estimates of statistical confidence in SNP-based assignments of offspring to pairs of parents. The method is implemented in the freely available software SNPPIT. We describe the method in detail, then assess its performance in a large simulation study using known allele frequencies at 96 SNPs from ten hatchery salmon populations. The simulations verify that the method is fast and accurate and that 96 well-chosen SNPs can provide sufficient power to identify the correct pair of parents from amongst millions of candidate pairs.
Impact of CIR processing for UWB radar distance estimation with the DW1000 transceiver

Automatic distance detection is essential for industrial safety processes, allowing detection of persons in unsafe zones, detecting obstacles nearby autonomous vehicles, etc. ultr-awideband (UWB) radar is a recent upcoming technology that is suitable for low-cost, device-free distance estimations to persons and obstacles. The excellent time properties of UWB allow the detection of distinct propagation paths from sender to receiver and reflecting objects. Currently, existing work utilizes dedicated UWB radar hardware. This paper focuses on off-the-shelf DW1000 UWB transceivers which have lower cost but also lower time resolution of the received channel impulse response (CIR). We analyze three data processing methods (ICIR, UCIR, and ACIR). Next, we analyze two distance estimation approaches in a realistic industrial environment: a mean based and a variance based. We demonstrate that selecting the best combination of data processing and distance estimator is crucial, allowing the detection of metal objects up to 900 cm with a mean accuracy of 9 cm, or the detection of persons with a mean absolute error of only 44 cm.
Statistical Applications in Genetics and Molecular Biology Fast Identification of Biological Pathways Associated with a Quantitative Trait Using Group Lasso with Overlaps

Where causal SNPs (single nucleotide polymorphisms) tend to accumulate within biological pathways, the incorporation of prior pathways information into a statistical model is expected to increase the power to detect true associations in a genetic association study. Most existing pathways-based methods rely on marginal SNP statistics and do not fully exploit the dependence patterns among SNPs within pathways. We use a sparse regression model, with SNPs grouped into pathways, to identify causal pathways associated with a quantitative trait. Notable features of our “pathways group lasso with adaptive weights” (P-GLAW) algorithm include the incorporation of all pathways in a single regression model, an adaptive pathway weighting procedure that accounts for factors biasing pathway selection, and the use of a bootstrap sampling procedure for the ranking of important pathways. P-GLAW takes account of the presence of overlapping pathways and uses a novel combination of techniques to optimise model estimation, making it fast to run, even on whole genome datasets. In a comparison study with an alternative pathways method based on univariate SNP statistics, our method demonstrates high sensitivity and specificity for the detection of important pathways, showing the greatest relative gains in performance where marginal SNP effect sizes are small.
The Studies on Mountain Mud-Rock Flow Critical Rainfall and Rainfall Zoning of Hubei Provice

By analyzing327 mountain mud-rock flow of Hubei provice in history,the spatial and temporal distributions of them was elicited.Then,80 typical cases since 1980 were collected and used to analyze the differences of rainfall between weather and hydrometric stations.the feasibility of compositive computational method about mountain mud-rock flow critical rainfall was discussed,this method was also used to compute weather stations critical rainfall of 36 cities or counties in Hubei Provice.Lastly,the results were combined with different frequencyes′ design rainfall and other rainstorm parameters,which were used to make the rainfall zoning of Hubei provice.
Geomorphology of the Ruby-East Humboldt Range, Nevada

A middle or late Pliocene open-valley stage in the Ruby-East Humboldt Range is recognized and described. The anomalous position of the drainage divide in places east of the range crest is explained in terms of the geomorphic evolution of the range. Pediments and terraces on the range flanks and in the adjoining basins are described, and those on the west side formed under a regime of through-flowing drainage are compared with those on the east side formed on the borders of hydrographically closed basins. Seven surfaces, the two highest being pediments and the others partial pediments and terraces, are recognized on the west flank of the range. The dissection of these surfaces is shown to be related to successive rejuvenations of the Humboldt River drainage. The exposure and dissection of surfaces on the east flank of the range are attributed chiefly to relative uplift of the range by faulting. These pediments and terraces have been formed between the middle Pleistocene and Recent. The origin of pediments under contrasting conditions is considered, and the conclusion is reached that different geologic, climatic, and topographic conditions impose a difference in the efficacy of processes of pedimentation. In this region lateral planation is dominant in areas of permanent streams and soft rocks; and rill wash, rain wash, and weathering are dominant in areas of hard rocks, ephemeral streams, and low mountain masses. Lateral erosion by streams accounts for approximately 40 per cent of the retreat of the mountain front, and approximately 60 per cent is due to weathering and various types of wash.
A Procedure for SyGuS Solution Fitting via Matching and Rewrite Rule Discovery

Syntax-guided synthesis (SyGuS) is a recent software synthesis paradigm in which an automated synthesis tool is asked to synthesize a term that satisfies both a semantic and a syntactic specification. We consider a special case of the SyGuS problem, where a term is already known to satisfy the semantic specification but may not satisfy the syntactic one. The goal is then to find an equivalent term that additionally satisfies the syntactic specification, provided by a context-free grammar. We introduce a novel procedure for solving this problem which leverages pattern matching and automated discovery of rewrite rules. We also provide an implementation of the procedure by modifying the SyGuS solver embedded in the CVC5 SMT solver. Our evaluation shows that our new procedure significantly outperforms the state of the art on a large set of SyGuS problems for standard SMT-LIB theories such as bit-vectors, arithmetic, and strings
Coupled Liquid Water, Water Vapor, and Heat Transport Simulations in an Unsaturated Zone of a Sandy Loam Field

Information on the coupled liquid water, water vapor, and heat transport under arable field conditions is still limited, particularly for unsaturated soils of semi-arid and arid regions such as New Mexico. HYDRUS-1D model was applied to evaluate various transport mechanisms associated with temporal variations in water content and soil temperature in the unsaturated zone of a sandy loam furrow-irrigated field located at Leyendecker Plant Science Research Center, Las Cruces, New Mexico. The model was calibrated using measured soil water content and soil temperature at 5-, 10-, 20-, and 50-cm depths during a 19-day period (day of the year [DOY] 85 to DOY 103, 2009) and validated for a 31-day period (DOY 104 to DOY 134, 2009). Measured and optimized soil hydraulic and thermal properties and hourly meteorological data were used in model simulations. HYDRUS-1D simulated water contents and soil temperatures correlated well with the measured data at each depth. The total liquid water flux, composed of isothermal and thermal liquid water flux, dominated the soil water movement during early periods after irrigation, whereas the contribution of total water vapor flux, composed of primarily thermal and much smaller isothermal water vapor flux, increased with increasing soil drying. During the soil drying process, the total liquid flux within 15-cm depth eventually changed to water vapor flux near the surface. The upward total liquid and vapor fluxes decreased from 5 cm, indicating that vapor flux was much higher in the layer near the soil surface. The total vapor flux in this unsaturated soil layer was approximately 10.4% of the total liquid and vapor fluxes during the simulation period.
Fabrication And Performance Evaluation Of An Evaporative Fabrication And Performance Evaluation Of An Evaporative Hollow Micropillar Module For Data Center Cooling Application Hollow Micropillar Module For Data Center Cooling Application

With the exponential growth of the Internet in the coming decade, data centers will be one of the largest consumers of electricity in many countries. In many data centers, thermal management systems could be just as power-consuming as IT equipment. Chillers in these thermal management systems are one of the highest power components. Microscale evaporation is a promising approach to dissipating high heat fluxes by minimizing thermal resistance between the junction temperature and ambient temperature, hence eliminating the need for chillers. Previous research has shown that droplets elevated by micropillars can limit the vapor diffusion confinement effect, which improves the evaporative heat transfer performance. For this thesis, an evaporative cooling module consisting of an array of hollow triangular micropillars was developed. This module allows microdroplets to be confined on top of the pillars' upper surface in optimal evaporative size. The thesis describes the device's fabrication process in a cleanroom environment, performance testing, and numerical simulations using COMSOL Multiphysics to illustrate the transport mechanisms behind our experiments.
Special Section on Drug Delivery Technologies — Minireview Liposomal Nanostructures for Drug Delivery in Gastrointestinal Cancers

Gastrointestinal (GI) cancers like liver, pancreatic, colorectal, and gastric cancer remain some of the most difficult and aggressive cancers. Nanoparticles like liposomes had been approved in the clinic for cancer therapy dating as far back as 1995. Over the years, liposomal formulations have come a long way, facing several roadblocks and failures, and advancing by optimizing formulations and incorporating novel design approaches to navigate therapeutic delivery challenges. The first liposomal formulation for a GI cancer drug was approved recently in 2015, setting the stage for further clinical developments of liposome-based delivery systems for therapies against GI malignancies. This article reviews the design considerations and strategies that can be used to deliver drugs to GI tumors, the wide range of therapeutic agents that have been explored in preclinical as well as clinical studies, and the current therapies that are being investigated in the clinic against GI malignancies.
Special Section on Drug Delivery Technologies A Polymeric Nanogel-Based Treatment Regimen for Enhanced Efficacy and Sequential Administration of Synergistic Drug Combination in Pancreatic Cancer s

Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal cancers. A combination of cisplatin (CDDP) and gemcitabine (Gem) treatment has shown favorable clinical results for metastatic disease; both are limited by toxicities and nontargeted delivery. More than 80% of PDAC aberrantly expresses the sialyl Tn (STn) antigen due to the loss of function of the core 1 b 3-Gal-T – specific molecular chaperone, a specific chaperone for the activity of core 1 b 3-galactosyltransferase or C1GalT. Here, we report the development of polymeric nanogels (NGs) loaded with CDDP and coated with an anti-STn antigen – specific antibody (TKH2 monoclonal antibody) for the targeted treatment of PDAC. TKH2-functionalized, CDDP-loaded NGs delivered a significantly higher amount of platinum into the cells and tumors expressing STn antigens. We also confirmed that a synergistic cytotoxic effect of sequential exposure of pancreatic cancer cells to Gem followed by CDDP can be mimicked by the codelivery of CDDP-loaded NGs (NG/CDDP) and free Gem. In a murine orthotopic model of PDAC, combined simultaneous treatment with Gem and targeted NG/CDDP significantly attenuated tumor growth with no detectable acute toxicity. Altogether, these results suggest that combination therapy consisting of Gem followed by TKH2-conjugated CDDP NGs induces highly syn- ergistic therapeutic efficacy against pancreatic cancer. Our results offer the basis for development of combination drug regimens using targeted nanomedicines to increase treatment effectiveness and improve outcomes of PDAC therapy. stained with hematoxylin and eosin (University of Nebraska Medical Center Tissue Sciences Facility). Statistical Analysis. Statistical comparisons for in vitro studies were done using the t test. One-way ANOVA was used for analysis of the mean bioluminescence signal intensity and body weight data. Differences in tumor metastasis between groups were analyzed using the two-tailed Fisher exact test. A statistically significant difference was considered at P , 0.05. Statistical analysis was performed using GraphPad 5 software.
Addressing Soil Degradation in EU Agriculture: Relevant Processes, Practices and Policies - Report on the project 'Sustainable Agriculture and Soil Conservation (SoCo)'

Agriculture occupies a substantial proportion of the European land, and consequently plays an important role in maintaining natural resources and cultural landscapes, a precondition for other human activities in rural areas. Unsustainable farming practices and land use, including mismanaged intensification as well as land abandonment, have an adverse impact on natural resources. Having recognised the environmental challenges of agricultural land use, the European Parliament requested the European Commission in 2007 to carry out a pilot project on "Sustainable Agriculture and Soil Conservation through simplified cultivation techniques" (SoCo). The project originated from a close cooperation between the Directorate-General for Agriculture and Rural Development (DG AGRI) and the Joint Research Centre (JRC). It was implemented by the Institute for Prospective Technological Studies (IPTS) and the Institute for Environment and Sustainability (IES). This report presents the findings of a stock-taking of the current situation with respect to soil degradation processes, soil-friendly farming practices and relevant policy measures within an EU-wide perspective. This overview includes the results of the survey on the national/regional implementation of EU policies and national policies, a classification of the described soil degradation processes, soil conservation practices and policy measures, and finally the outcome of the Stakeholder Workshop which took place on 22 May 2008 in Brussels.
Spiking Neural Network-based Control Applied to an Underactuated System

This paper presents the problem of stabilizing an underactuated system, the Ball and Plate platform, by means of a neuromorphic-inspired control. The proposed architecture makes use of Spiking Neural Networks (SNNs) in combination with the Neural Engineering Framework (NEF) to accomplish regularization and trajectory tracking. Simulation results for both the proposed SNN controller and its conventional (non-neural) counterpart are presented and qualitatively compared. The results show that the SNN controller effectively tracks a desired trajectory with minimal tracking errors. The practical considerations for implementing a fully neuromorphic real-time application of the proposed approach are discussed as well.
Conservation and land use planning applications in Gabon, Central Africa

Spatial prioritization and systematic conservation planning methods are designed to improve land use decisions and conservation outcomes, yet remain underutilized in many biologically-rich places that need them most. This thesis applies the theory and methods developed in the discipline of spatial prioritization to conservation and land use decisions in the Central African country of Gabon. Creating a spatial information base of priority species, habitats and land uses in a region that is notoriously data-poor, I reveal that many features important for both conservation and natural resource production are highly localized; their coincidence has important implications for management. Setting conservation targets for species and habitats, I find that representation in existing protected areas is relatively low, and identify a number of near-optimal solutions that meet all targets, with minimal impact on land used for local livelihoods. I distill these solutions down to a handful of critical biodiversity sites that are top priority to protect, and make management actions explicit for the species and habitats they contain. To make the work more widely applicable, I also develop a novel method to identify where field surveys are most likely to improve decisions about protected area expansion, providing decision-makers with more options of places that could be protected to achieve conservation goals. This study contributes to the research, development and practice of conservation prioritization and spatial planning, particularly in data-poor contexts like Gabon, which still have a wealth of biodiversity, and need to carefully plan for its conservation alongside development.
Grigory Rasputin in the Mirror of Western Screen

The article argues the approaches to the analysis of Western screen stereotypes of Grigory Rasputin as a kind of a metaphor of Russia's image in Western interpretation. Thus, as a result of the analysis it can be concluded that the Western film interpretations using Grigory Rasputin's image construct an extremely simplistic image of the country. Consequently, a barbaric, unpredictable, rebellious, mystical, and most importantly – a strange, not compatible with the normal US-European way of life, image of Russia is created.
Estimating the seroprevalence of t. Parva infection and determination of associated risk factors in the cattle population of Mbeere District, Kenya

xv CHAPTER 1: INTRODUCTION. 1 1.1. Background. 1 1.2. Study objectives. 5 1.2.1. Overall objective. 5 1.2.2. Specific objectives. 6 CHAPTER 2: LITERATURE REVIEW. 7 2.1. Livelihoods and livestock. 7 2.2. Farming system in Mbeere District.8 2.3. Tick-borne diseases and their economic importance. 10 2.4. Tick-borne diseases aetiological research. 12 2.4.1. The concepts of causality, risk and web of causation. 12 2.4.2. Assessing tick-borne diseases at multiple levels of population organization. 14 2.5. East Coast fever. 16 2.5.1. Definition and aetiology. 16 2.5.2. Disease distribution. 16 2.5.3. Life cycle. 18 2.5. 4. Risk factors for ECF. 19 2.5. 4.1. Causative agent risk factors for ECF. 21 2.5. 4.2. Tick vector and ECF transmission dynamics. 23 iv 2.5. 4.3. Vertebrate host factors for ECF. 25 2.5. 4.4. Herd-level management risk factors in relation to disease control. 27 2.5. 4.5. Area-level risk factors for ECF. 29 2.5. 5. Epidemiological states of ECF.33 2.5. 5.1. Endemic stability. 33 2.5. 5.2. Endemic instability. 34 2.5. 5.3. Epidemic East Coast fever. 34 2.5. 6. Clinical syndrome. 35 2.5. 7. Diagnosis. 35 2.5. 7.1. Clinical, parasitological and molecular diagnosis. 35 2.5. 7.2. Serodiagnosis . 36 2.5. 7.2.1. Indirect fluorescent antibody test. 36 2.5. 7.2.2. Enzyme-linked immunosorbent Assay (ELISA). 36 2.5. 8. Control. 38 2.5. 8.1. Treatment. 38 2.5. 8.2. Tick control. 39 2.5. 8.3. Immunization . 39 CHAPTER 3: GENERAL MATERIALS AND METHODS. 40 3.1. Study site . 40 3.1.1. Location and description Mbeere District.40 3.1.2. Topography of Mbeere District. 41 3.1. 3. Climate of Mbeere District. 42 3.2. Study design. 42 3.2.1. Selection of sub-locations and farms. 42 3.2.2. Sample size and selection of animals.43 3.3. Data handling and management. 45 3.3.1. Farming system data collection. 45 3.3.2. Animal data collection. 46 3.3.3. Statistical analyses. 46 CHAPTER 4: DESCRIPTION AND CHARACTERISTICS OF TRADITIONAL SMALLHOLDER CROP-LIVESTOCK PRODUCTION SYSTEM IN MBEERE DISTRICT, KENYA. 48 4.