Miracle-dz/UniFAR-FTUs huggingface dataset:
Development of Adaptive Management Tools to Guide Habitat Allocations for At-Risk Species

Abstract : The Department of Defense is increasingly engaging landowners outside installation boundaries to help protect biodiversity at a landscape scale. Such activities include the acquisition of recovery habitat for species at risk and cooperation with conservation partners. The objectives of this project were to 1) contrast the ability of data provided by different conservation partners to reduce uncertainty in dynamic landscape simulation models (i.e., individual-based, spatially explicit population models, IB-SEPMs); 2) apply Decision Analysis to identify the most cost-effective allocation of habitat, given uncertainty in the IB-SEPM; and 3) contrast the ability of the technique to be applied to well-studied (i.e., red-cockaded woodpecker) and poorly-studied (gopher tortoise) species. The study found that the natural history of the red-cockaded woodpecker was sufficiently understood to prioritize habitat allocations to protect the abundance of the species but not to protect genetic diversity of the species. In contrast, for the gopher tortoise this study concluded that we do not sufficiently understand the species natural history traits to protect either abundance or genetic diversity. The methods developed here provide an approach for managing habitat area and connectivity that includes uncertainty regarding species natural history, helps to prioritize collection of monitoring data, and supports cost-effective decision making.
The Babar Collaboration

We present a preliminary measurement of the time-dependent CP -violating asymmetry parameters Sππ and Cππ in neutral B decays to the π ±π∓ CP eigenstate, and an updated preliminary measurement of the charge asymmetry AKπ in B → K±π∓ decays. Event yields and CP -violation parameters are determined simultaneously from a multidimensional unbinned maximum likelihood fit. In a data sample consisting of approximately 33 million Υ (4S) → BB decays collected with the BABAR detector at the SLAC PEP-II asymmetric B Factory, we find 65 −11 π ±π∓ and 217±18 K±π∓ candidates and measure Sππ = 0.03 +0.53 −0.56±0.11, Cππ = −0.25 −0.47±0.14, and AKπ = −0.07±0.08±0.02, where the first error is statistical and the second is systematic. Submitted to the 20 International Symposium on Lepton and Photon Interactions at High Energies, 7/23–7/28/2001, Rome, Italy Stanford Linear Accelerator Center, Stanford University, Stanford, CA 94309 Work supported in part by Department of Energy contract DE-AC03-76SF00515.
Measurement of CP-violating asymmetries in the neutral B meson decaying to the ρπ state using a time-dependent Dalitz plot analysis

In the standard model (SM), CP violation arises from an irreducible phase in the CabibboKobayashi-Maskawa (CKM) matrix. A Dalitz plot analysis of the decay B → ρπ → πππ offers a unique way to determine the angle φ2 in the CKM unitarity triangle without discrete ambiguities (for φ2 in the range between 0 and π), which cannot be obtained from analyses of other modes sensitive to φ2 such as B → ππ or B → ρρ. The Dalitz plot analysis uses isospin and takes into account a possible contamination from b → d penguin transitions. In addition, using measurements of the related charged decay modes B → ρπ and B → ρπ provides further improvement of the φ2 determination. In this thesis, we present the result of time-dependent Dalitz plot analysis in B → πππ decays and a constraint on φ2. We use a 414 fb −1 data sample that contains 449×106BB̄ pairs collected on the Υ(4S) resonance. The data were taken at the KEKB collider and collected with the Belle detector. By the Dalitz plot analysis, we constrain the relative sizes and phases of the complex amplitudes of B(B) → ρπ, ρπ, and ρπ decays, which are denoted by (A)+, (A)−, and ( A ) , respectively. The amplitudes are related to φ2 through an isospin relation by e2 = A +A + 2A A+ +A− + 2A0 . Combining our analysis with information on charged B decay modes, we perform a full Dalitz and isospin analysis for the first time and obtain a constraint on the CKM angle φ2, 68 < φ2 < 95 ◦ , as the 68.3% confidence interval consistent with the standard model (SM). A large SMdisfavored region also remains. This result is combined with the other measurements from B → ππ and B → ρρ, and its consistency with the SM expectation is examined; we confirm they are consistent with each other at a precision of ∼ 7.
Multilevel Models and Inequality in Viet Nam

This paper proposes to investigate inequality in Viet Nam from the point of view of a study of the urban/rural gap by means of a multilevel model. Using data from the Viet Nam Household Living Standards Survey of 2002, the paper constructs a multilevel model, yielding random effects in the urban/rural gap which can be seen as location-specific random contributions to the urban/rural gap above and beyond the effects of known location characteristics, such as the level of education of the population, etc. The paper also demonstrates how the multilevel model can be used to obtain small area estimates at the commune level.
Searching for Efficient Operating Conditions of Wastewater Treatment Processes

Changing the configuration of a system to treat wastewater has a major influence on the entire process, by modifying operating characteristics of system and the microbial populations involved in treatment processes. The system under study has two bioreactors in series, each followed by a separator, a recycle and a purge. Recycle and purge ratios were used from 0.1 to 1, for the former, and 0.001 to 0.01, for the latter. At the same time, the series of reactor has an external recycle, which could have a ratio from 0 to 3. The overall system performance and the diversity of the microbial communities in the reactors can be affected by working on different operating conditions. Two types of effects were investigated in this study with respect to the performance of a biological treatment process for wastewater: topological, when the configuration of the systems changes, and operational, when recycle and purge ratios change for a given topology.
Set5 and Set1 cooperate to repress gene expression at telomeres and retrotransposons

A complex interplay between multiple chromatin modifiers is critical for cells to regulate chromatin structure and accessibility during essential DNA-templated processes such as transcription. However, the coordinated activities of these chromatin modifiers in the regulation of gene expression are not fully understood. We previously determined that the budding yeast histone H4 methyltransferase Set5 functions together with Set1, the H3K4 methyltransferase, in specific cellular contexts. Here, we sought to understand the relationship between these evolutionarily conserved enzymes in the regulation of gene expression. We generated a comprehensive genetic interaction map of the functionally uncharacterized Set5 methyltransferase and expanded the existing genetic interactome of the global chromatin modifier Set1, revealing functional overlap of the two enzymes in chromatin-related networks, such as transcription. Furthermore, gene expression profiling via RNA-Seq revealed an unexpected synergistic role of Set1 and Set5 in repressing transcription of Ty transposable elements and genes located in subtelomeric regions. This study uncovers novel pathways in which the methyltransferase Set5 participates and, more importantly, reveals a partnership between Set1 and Set5 in transcriptional repression near repetitive DNA elements in budding yeast. Together, our results define a new functional relationship between histone H3 and H4 methyltransferases, whose combined activity may be implicated in preserving genomic integrity.
”Menage à trois”: the presence/absence of thyme shapes the mutualistic interaction between the host plant [i]Medicago truncatula[/i] (Fabaceae) and its symbiotic bacterium [i]Sinorhizobium meliloti[/i]

The long-term maintenance of specialized mutualisms remains an evolutionary puzzle. Recent focus has been on factors governing the stability of these mutualisms, including sanctions by the host, partner choice, and coevolutionary constraint, that is, the genetic correlation ( r G ) between ﬁtness of both partners. So far these studies have been typically carried out in a single environment. Here, we ask if the genetic correlation between ﬁtness of the host plant Medicago truncatula (Fabaceae) and its bacterial symbiont Sinorhizobium meliloti is affected by the presence/absence of a monoterpene (carvacrol) leached into the soil by Thymus vulgaris —a common plant of the Mediterranean vegetation, often co-occuring with Medicago . We show that the presence of carvacrol in the soil dramatically affects ﬁtness of the rhizobial partner and increases the magnitude of r G between plant and rhizobia ﬁtness ( r G = 0.02
Carbon Sequestration Potential of Agricultural Crops in Designed Plant Growth Chamber

Aim: Climate change is becoming one of the major global environment concerns. The earth’s climate is predicted to change due to release of greenhouse gases and there is an urgent need for stabilizing the increasing levels of carbon dioxide in atmosphere. Soil carbon sequestration is considered as one of the promising options for mitigating the climate change impacts. The aim of the current study is to assess the carbon sequestration potential of the crops of the agricultural importance at elevated levels of CO 2 in designed plant growth chamber. Place and Duration of Study: School of Environment and Sustainable Development, Central University of Gujarat, India, between November 2013 to June 2014. Methodology: Plant growth chamber has been designed of dimension 66◊24◊25 inches for assessing the carbon sequestration potential of the selected agricultural crops Triticum aestivum, Sorghum vulgare and Vigna radiata in green house. The plants were grown using the pot culture technique in mycorrhizal soil. The CO 2 was induced into the plant growth chamber after every five days at the rate of 5 Litres per minute to maintain the level of carbon dioxide upto 500±50 ppm into the plant growth chamber and plant’s growth was studied. Soil’s physico-chemical parameters, plant’s morphological and biochemical characteristics were studied in each plant. Results: The study reveals the carbon content estimated in the form of organic carbon, total carbon and organic matter was high in Vigna radiata at elevated CO 2 levels, than ambient levels, followed by Sorghum vulagare and Triticum aestivum. Also organic nitrogen accumulation was increased in response of elevated CO2 conditions, highest being found in samples of Vigna radiata . Morphological and biochemical characteristics of crops also got influenced under elevated CO 2 levels. Plant height and plant biomass accumulation was found to be higher in Triticum aestivum , followed by Sorghum vulgare and Vigna radiata , whereas shoot and root length was Original Research Article
Landform signature of the Laurentide and Cordilleran ice sheets across Alberta during the last glaciation

Government geological survey maps and research publications have portrayed the distribution of glacial landforms associated with the advance and retreat of the Laurentide and Cordilleran ice sheets across Alberta at a local, regional, and continental scale. To date, this information has not been systematically synthesized into a single compilation at a consistent scale. Although this original work provided valuable information to constrain reconstructions of former ice sheet extent, configuration, and flow geometry, its derivation primarily from the interpretation of aerial photographs and the Shuttle Radar Topography Mission 90 m digital elevation model (DEM) may result in methodological inconsistencies and spatial biases. These biases, together with challenges associated with geomorphic mapping in densely forested areas of western and northern Alberta limit the usefulness of previous mapping when applied to inversion-based ice sheet reconstructions, which have specific input data demands. Recently, ligh.
Requirements Analysis in Distributed Software Engineering Education – An Experience Report

In March 2001, two student teams, one in Melbourne, Australia, and one in Dortmund, Germany, started a common software engineering project to develop an electronic management tool for the support of scientific conferences. Both teams had to take part in all key activities of this project. The different deliverables had to be matched periodically in order to ensure the development of a common tool. In doing so, the teams had to deal with typical communication problems caused by different time zones, geographical distribution, language issues, and different approaches to requirements analysis. This paper presents the experiences and the lessons learned during requirements elicitation in the context of a distributed software engineering education project.
Title Plate-based transfection and culturing technique for genetic manipulation of Plasmodium falciparum Permalink

Genetic manipulation of malaria parasites remains an inefficient, time-consuming and resource-intensive process. Presented here is a set of methods for 96-well plate-based transfection and culture that improve the efficiency of genetic manipulation of Plasmodium falciparum. Compared to standard protocols plate-based transfection requires 20-fold less DNA, transient transfection efficiency achieved is approximately seven-fold higher, whilst stable transfection success rate is above 90%. Furthermore the utility of this set of protocols to generate a knockout of the PfRH3 pseudogene, screened by whole-cell PCR, is demonstrated. The methods and tools presented here will facilitate genome-scale genetic manipulation of P. falciparum.
Multiple View Geometry in Computer Vision

From the Publisher: A basic problem in computer vision is to understand the structure of a real world scene given several images of it. Recent major developments in the theory and practice of scene reconstruction are described in detail in a unified framework. The book covers the geometric principles and how to represent objects algebraically so they can be computed and applied. The authors provide comprehensive background material and explain how to apply the methods and implement the algorithms directly.
Processing and Analyzing Advanced Hyperspectral Imagery Data for Identifying Clay Minerals .A Case Study

Spectral analyses as one of the most advanced remote sensing techniques were used to identify mineralogy of the clay fractions in South Port Said plain, Egypt. Different spectral processes have been used to execute the prospective spectral analyses. These processes include 1-The reflectance calibration of Hyperspectral data belonging to the studied area, 2- Using the Minimum Noise Fraction (MNF) transformation.3-Creating the pixel purity index (PPI) which used as a mean of finding the most "spectrally pure", extreme, pixel in hyperspectral images. Making conjunction between the Minimum Noise Fraction Transform (MNF) and Pixel Purity Index (PPI) tools through 3-D visualization offered capabilities to locate, identify and cluster the purest pixels and most extreme spectral responses in a data set. To identify the clay minerals of the studied area the extracted unknown spectra of the purest pixels was matched to pre-defined (library) spectra providing score with respect to the library spectra. Three methods namely, Spectral Feature Fitting (SFF),Spectral Angle Mapper (SAM) and Binary Encoding (BE) were used to produce score between 0 and 1, where the value of 1 equal a perfect match showing exactly the mineral type. In the investigated area four clay minerals could be identified i.e. Vermiculite, Kaolinite, Montmorillinite and Illite recording different scores related to their abundance in the soils. In order to check the validity and accuracy of the obtained results, X ray diffraction analysis was applied on surface soil samples covering the same locations of the signature end- members that derived from hyperspectral image. Highly correlated and significant results were obtained using the two approaches (spectral signatures and x-ray diffraction).
Interpolation and assimilation methods for European scale air quality assessment and mapping Part I: Review and recommendations

The European Topic Centre on Air and Climate Change (ETC/ACC) is a consortium of European institutes under contract of the European Environmental Agency Front page picture Combined rural and urban concentration map of the annual average PM 10 for the year 2001 based on spatial interpolated concentration fields and measured values at the indicated measuring points (units in µg.m-3 .days). (The figure is taken from ETC/ACC Technical Paper 2005/8, Annex Figure 6A. It represents the combined map as created by merging the interpolated rural map (combination of measured values with EMEP model, altitude and sunshine duration, using linear regression and ordinary kriging of residuals) and the interpolated urban map (using interpolation of urban increment Delta by ordinary kriging). Countries with interpolation based on additional data only: BG, GR, HR, HU, RO. Countries with missing population density information and therefore excluded from the mapping calculations: DISCLAIMER This ETC/ACC Technical Paper has not been subjected to European Environment Agency (EEA) member state review. It does not represent the formal views of the EEA.
Flooded Communities

This article uses the post-Katrina migration as an exogenous shock to test theories of racial threat while minimizing concerns about selection bias. Drawing in part on a new survey of 3,879 respondents, it demonstrates that despite the national concern about issues of race and poverty following Katrina, people in communities that took in evacuees became less supportive of spending to help the poor and African Americans. The results suggest a novel hypothesis that threatened responses to newcomers hinge on both local conditions and the frames that develop around their arrival.
The impacts of drainage, nutrient status and management practice on the full carbon balance of grasslands on organic soils in a maritime temperate zone

Temperate grasslands on organic soils are diverse due to edaphic properties but also to regional management practices and this heterogeneity is reflected in the wide range of greenhouse gas (GHG) flux values reported in the lit- erature. In Ireland, most grasslands on organic soils were drained several decades ago and are managed as extensive pastures with little or no fertilisation. This study describes a 2-year study of the net ecosystem carbon balance (NECB) of two such sites. We determined GHG fluxes and water- borne carbon (C) emissions in a nutrient-rich grassland and compared it with values measured from two nutrient-poor or- ganic soils: a deep-drained and a shallow-drained site. Car- bon dioxide (CO2), methane (CH4) and nitrous oxide (N2O) fluxes were determined using the chamber technique, and flu- vial C fluxes were estimated by combining drainage water concentrations and flows. The nutrient-rich site was an annual source of CO2 (233 g C m 2 yr 1 ), CH4 neutral, and a small source of N2O (0.16 g N2O-N m 2 yr 1 ). Net ecosystem exchange (NEE) at the shallow-drained nutrient-poor site was 89 and 99 g C m 2 yr 1 in Years 1 and 2 respectively, and NEE at the deep-drained nutrient-poor site was 85 and 26 g C m 2 yr 1 respectively. Low CH4 emissions (1.3 g C m 2 yr 1 ) were recorded at the shallow-drained nutrient-poor site. Fluvial exports from the nutrient-rich site totalled 69.8 g C m 2 yr 1 with 54 % as dissolved organic C.
Trends in Abundance of Australian Sea Lions, Neophoca cinerea, at Seal Bay, Kangaroo Island, South Australia

Pups of the Australian sea lion have been counted at Seal Bay for 20 pupping seasons, 1973-74 to 2002-03. Temporal changes in counts of live pups over the course of each pupping season were fitted to Gaussian (nor mal) curves to determine objectively the date when pup numbers reached their peak. The mean interval between pupping seasons was 532 ± 31 days (i.e., 17.5 months). Maximum counts of live pups for 13 pupping seasons averaged 144 (s.d. 14) from 1985 (from when data quality was
Undercalibrating in goal‐directed therapy?

Sir, We read with interest, the investigations of Bisgaard et al. Benefits of goal-directed therapy continue to be discussed, along with the methods by which it should be assessed. Bisgaard et al. concluded that perioperative individualised goal-directed therapy does not affect post-operative complications, or length of intensive care unit and hospital stay, in open elective abdominal aortic surgery. The study protocol states that LiDCOplus (LiDCO Group plc, London, UK) recalibration occurred twice in the study period; firstly, prior to induction of general anaesthesia, and secondly, following unclamping of the aorta. The findings from this recalibration suggest that there was no significant change in calibration factor (CF) between these two times. However, the findings from Beattie et al. suggest that recalibration is necessary throughout non-cardiac surgery as CF varies during the procedure. This study protocol had six points of recalibration, following the initial baseline calibration prior to induction: after establishing epidural anaesthesia, following induction of general anaesthesia, following aortic crossclamping, after aortic unclamping, at skin closure, and following return of spontaneous ventilation and removal of endotracheal tube. The findings indicate that there is a significant fall in CF on aortic cross-clamping, leading to an overestimation of stroke volume and cardiac output unless recalibration is undertaken. Conversely, CF was significantly higher following epidural and general anaesthesia compared with the CF prior to induction. This would underestimate the stroke volume and cardiac output if recalibration did not occur. Beattie et al. concluded in order to obtain absolute values of cardiac output, recalibration of the LiDCOplus monitor is necessary during abdominal aortic surgery as the magnitude of changes in CF varies between patients, and this cannot be predicted. Potential errors such as the administration or withholding of fluid or drug therapy could occur as a result of this overor underestimation when frequent recalibration does not occur. It would appear that before dismissing the potential advantages of goal-directed therapy in abdominal aortic aneurysm patients, a further study, including the calibration outlined by Beattie et al., should be performed. Conflict of interest: None.
2 Putting Knowledge in Topic Models

Topic models have been used extensively as a tool for corpus exploration, and a cottage industry has developed to tweak topic models to better encode human intuitions or to better model data. However, creating such extensions requires expertise in machine learning unavailable to potential end-users of topic modeling software. In this work, we develop a framework for allowing users to iteratively refine the topics discovered by models such as latent Dirichlet allocation (LDA) by adding constraints that enforce that sets of words must appear together in the same topic. We incorporate these constraints interactively by selectively removing elements in the state of a Markov Chain used for inference; we investigate a variety of methods for incorporating this information and demonstrate that these interactively added constraints improve topic usefulness for simulated and actual user sessions.