Miracle-dz/UniFAR-FTUs huggingface dataset:
Emerging Issues in Population Viability Analysis

Abstract: Population viability analysis ( PVA) has become a commonly used tool in endangered species management. There is no single process that constitutes PVA, but all approaches have in common an assessment of a population's risk of extinction (or quasi extinction) or its projected population growth either under current conditions or expected from proposed management. As model sophistication increases, and software programs that facilitate PVA without the need for modeling expertise become more available, there is greater potential for the misuse of models and increased confusion over interpreting their results. Consequently, we discuss the practical use and limitations of PVA in conservation planning, and we discuss some emerging issues of PVA. We review extant issues that have become prominent in PVA, including spatially explicit modeling, sensitivity analysis, incorporating genetics into PVA, PVA in plants, and PVA software packages, but our coverage of emerging issues is not comprehensive. We conclude that PVA is a powerful tool in conservation biology for comparing alternative research plans and relative extinction risks among species, but we suggest caution in its use: (1) because PVA is a model, its validity depends on the appropriateness of the model's structure and data quality; (2) results should be presented with appropriate assessment of confidence; (3) model construction and results should be subject to external review, and (4) model structure, input, and results should be treated as hypotheses to be tested. We also suggest (5) restricting the definition of PVA to development of a formal quantitative model, (6) focusing more research on determining how pervasive density‐dependence feedback is across species, and (7) not using PVA to determine minimum population size or (8) the specific probability of reaching extinction. The most appropriate use of PVA may be for comparing the relative effects of potential management actions on population growth or persistence.
The Impact Of Web-Based Diabetes Risk Calculators On Information Processing and Risk Perceptions

As consumer demand for online health information grows, many organizations are providing personalized and interactive health risk communication tools. In response, there is a need to better understand how effective these features are in influencing user attention, information processing and risk perceptions. This study randomly assigned 100 middle-aged and elderly adult users to one of three versions of an experimental type 2 diabetes "risk calculator" in order to determine if personalized risk estimates and interactive risk feedback impact usage behavior and beliefs about future diabetes onset. Results suggest that personalization and interactive features did not lead to increases in user attention or systematic information processing. The experiment provided only modest evidence that personalization was related to increased accuracy in absolute diabetes risk perceptions. Future studies are warranted to more precisely explain the descriptive and normative implications when laypersons use web-based risk communication tools.
A First Investigation on Mongolian Information Retrieval

In this paper we present an attempt to build a test collection for Mongolian IR as well as some preliminary tests about the key issues in Mongolian Information Retrieval: using a stoplist and using word stemming. Our preliminary tests will show that while these basic operations on Mongolian can bring slight improvements in retrieval effectiveness, many problems remain. The results using stemming and stoplist show that the stemming can potentially lead to some gain in retrieval effectiveness; The stoplist slightly improve retrieval effectiveness, but it can reduce the index significantly.
広島大学学術情報リポジトリ Hiroshima University Institutional

Task-Irrelevant Abstract In this study, by manipulating perceptual load, we investigated whether socially anxious people process task-irrelevant, non-emotional, natural scenes. When attention was directed to letters and perceptual load was low, task-irrelevant natural scenes were processed, as evidenced by repetition priming effects, in both high and low socially anxious people. In the high perceptual load condition, repetition-priming effects decreased in participants with low social anxiety, but not in those with high social anxiety. The results were the same when attention was directed to pictures of animals: even in the high perceptual load condition, high socially anxious participants processed task-irrelevant natural scenes, as evidenced by flanker effects. However, when attention was directed to pictures of people, task-irrelevant natural scenes were not processed by participants in either anxiety group, regardless of perceptual load. These results suggest that high socially anxious individuals could not inhibit task-irrelevant natural scenes under conditions of high perceptual load, except when attention was focused on people.
Two‐level preconditioning of discontinuous Galerkin approximations of second‐order elliptic equations

This paper reviews some known and proposes some new preconditioning methods for a number of discontinuous Galerkin (or DG) finite element approximations for elliptic problems of second order. Nested hierarchy of meshes is generally assumed. Our approach utilizes a general two‐level scheme, where the finite element space for the DG method is decomposed into a subspace (viewed as an auxiliary or ‘coarse’ space), plus a correction which can be handled by a standard smoothing procedure. We consider three different auxiliary subspaces, namely, piecewise linear C0‐conforming functions, piecewise linear functions that are continuous at the centroids of the edges/faces (Crouzeix‐Raviart finite elements) and piecewise constant functions over the finite elements. To support the theoretical results, we also present numerical experiments for 3‐D model problem showing uniform convergence of the constructed methods. Copyright © 2006 John Wiley & Sons, Ltd.
Molecular Analysis of a Leprosy Immunotherapeutic Bacillus Provides Insights into Mycobacterium Evolution

Background Evolutionary dynamics plays a central role in facilitating the mechanisms of species divergence among pathogenic and saprophytic mycobacteria. The ability of mycobacteria to colonize hosts, to proliferate and to cause diseases has evolved due to its predisposition to various evolutionary forces acting over a period of time. Mycobacterium indicus pranii (MIP), a taxonomically unknown ‘generalist’ mycobacterium, acts as an immunotherapeutic against leprosy and is approved for use as a vaccine against it. The large-scale field trials of this MIP based leprosy vaccine coupled with its demonstrated immunomodulatory and adjuvant property has led to human clinical evaluations of MIP in interventions against HIV-AIDS, psoriasis and bladder cancer. MIP, commercially available as ‘Immuvac’, is currently the focus of advanced phase III clinical trials for its antituberculosis efficacy. Thus a comprehensive analysis of MIP vis-à-vis evolutionary path, underpinning its immanent immunomodulating properties is of the highest desiderata. Principal Findings Genome wide comparisons together with molecular phylogenetic analyses by fluorescent amplified fragment length polymorphism (FAFLP), enterobacterial repetitive intergenic consensus (ERIC) based genotyping and candidate orthologues sequencing revealed that MIP has been the predecessor of highly pathogenic Mycobacterium avium intracellulare complex (MAIC) that did not resort to parasitic adaptation by reductional gene evolution and therefore, preferred a free living life-style. Further analysis suggested a shared aquatic phase of MAIC bacilli with the early pathogenic forms of Mycobacterium, well before the latter diverged as ‘specialists’. Conclusions/Significance This evolutionary paradigm possibly affirms to marshal our understanding about the acquisition and optimization of virulence in mycobacteria and determinants of boundaries therein.
3D SURFACE RECONSTRUCTION BASED ON COMBINED ANALYSIS OF REFLECTANCE AND POLARISATION PROPERTIES: A LOCAL APPROACH

An image-based 3D surface reconstruction technique based on simultaneous evaluation of reflectance and polarisation features is introduced in this paper. The proposed technique is suitable for single and multi-image (photopolarimetric stereo) analysis. It is especially suited for the difficult task of 3D reconstruction of rough metallic surfaces with non-Lambertian reflectance. The reflectance and polarisation properties are used to determine the surface gradients in dividually for each image pixel. The presented multi-image technique is invariant to variations of the surface albedo. We evaluate our algorithm based on synthetic ground truth data as well as on a raw forged iron surface. The results we obtain for the real world example demonstrate the applicability of our method in the domain of industrial quality inspection.
Atrial Natriuretic Peptide Dose-Dependently Inhibits Pressure Overload–Induced Cardiac Remodeling

We hypothesized that a single copy of the proatrial natriuretic peptide gene (Nppa+/−) would not be adequate to protect heterozygous mice against exaggerated cardiac hypertrophy and remodeling after pressure-overload stress. Nppa+/+, Nppa+/−, and Nppa−/− mice were subjected to sham surgery or transverse aortic constriction and fed a basal salt diet. Heart weight varied inversely with Nppa gene load by 1 week after either surgery. Fractional shortening did not differ among genotypes at baseline and fell in Nppa−/− mice only after transverse aortic constriction. There was a graded response in collagen deposition related to atrial natriuretic peptide (ANP) expression after either surgery. A robust interstitial and perivascular fibrosis was noted in Nppa−/− and Nppa+/− but not in Nppa+/+ mice after transverse aortic constriction. Our findings are consistent with a growing body of evidence that ANP is an important modulator of cardiac hypertrophy and remodeling in response to hemodynamic stress. The observation that partial ANP deficiency results in exaggerated hypertrophy and remodeling after pressure overload suggests that genetic or environmental variation in ANP levels may play a role in the development of cardiac hypertrophy, remodeling, and failure in humans.
Mechanisms of inhibition of return: Brain, behavior, and computational modeling

Inhibition of return (IOR) is a cognitive phenomenon whereby reaction times (RTs) are slower to cued relative to uncued targets at cue-target onset asynchronies (CTOAs) greater than approximately 300 ms. One important theory of IOR proposes that there are two mutually exclusive forms of IOR, with an attentional/perceptual form arising when the oculomotor system is actively suppressed, and a motoric form arising when it is engaged (Taylor & Klein, 2000). Other theories propose that IOR is the result of multiple, additive neural mechanisms (Abrams & Dobkin, 1994). Here, we have performed computational simulations and empirical investigations in an attempt to reconcile these two competing theories. Using a dynamic neural field (DNF) model of the intermediate layers of the superior colliculus (iSC), we have modeled both a sensory adaptation mechanism of IOR, and a motoric mechanism resulting from the aftereffects of saccadic eye movements. Simulating these mechanisms, we replicated behavior and neurophysiology in a number of variations on the traditional cue-target paradigm (Posner, 1980). Predictions driven by these simulations have led to the proposal of many behavioral and neuroimaging experiments which further examine the plausibility of a 2mechanisms theory of IOR. Contrary to our original predictions, we demonstrated that saccades are biased away from cued targets in a paired target saccade averaging paradigm, even at short CTOAs. In paradigms thought to recruit both sensory and motoric mechanisms, we robustly demonstrated that there are at least two independent, additive mechanisms of IOR when tasks require saccadic responses to targets. When similar paradigms were tested with manual responses to targets, additivity effects did not hold, implying that the motoric mechanism of IOR does not transfer from the oculomotor to skeletomotor systems. Furthermore, across numerous experiments using event-related potential (ERP) techniques, we have demonstrated that P1 component reductions are neither necessary, nor sufficient, for the behavioral exhibition of IOR. We propose that a comprehensive framework for behavioral IOR must include (at least) four independent neural mechanisms, differentially active depending on circumstances, including sensory adaptation, saccadic aftereffects, local inhibition, and cortical habituation.
Stimulation of sister chromatid exchanges and mutation by aflatoxin B1‐DNA adducts in Saccharomyces cerevisiae requires MEC1 (ATR), RAD53, and DUN1

The hepatocarcinogen aflatoxin B1 (AFB1) is a potent recombinagen but weak mutagen in the yeast Saccharomyces cerevisiae. AFB1 exposure induces DNA damage‐inducible genes, such as RAD51 and those encoding ribonucleotide reductase (RNR), through a MEC1 (ATR homolog)‐dependent pathway. Previous studies have indicated that MEC1 is required for both AFB1‐associated recombination and mutation, and suggested that AFB1‐DNA adducts are common substrates for recombination and mutagenesis. However, little is known about the downstream effectors of MEC1 required for genotoxic events associated with AFB1 exposure. Here we show that AFB1 exposure increases frequencies of RAD51‐dependent unequal sister chromatid exchange (SCE) and activates Rad53 (CHK2). We found that MEC1, RAD53, and DUN1 are required for both AFB1‐associated mutation and SCE. Deletion of SML1, which encodes an inhibitor of RNR, did not suppress the DUN1‐dependent requirement for AFB1‐associated genetic events, indicating that higher dNTP levels could not suppress the dun1 phenotype. We identified AFB1‐DNA adducts and show that approximately the same number of adducts are obtained in both wild type and rad53 mutants. Since DUN1 is not required for UV‐associated mutation and recombination, these studies define a distinct role for DUN1 in AFB1‐associated mutagenesis and recombination. We speculate that AFB1‐associated DNA adducts stall DNA replication, a consequence of which can either be mutation or recombination. © 2008 Wiley‐Liss, Inc.
Some physiological aspects of aging in man.

the logarithm of the is the age of or 50 the are essentially straight with a constant Comparison of the curves for where mortality rates are high, with those of the United States,2 indicates two major (a) the slopes of the curves are strikingly similar, and (b) the curve for the United States is displaced to the Thus, a given rate of mortality attained in India at ages of the
Global Ecological Pattern of Ammonia-Oxidizing Archaea

Background The global distribution of ammonia-oxidizing archaea (AOA), which play a pivotal role in the nitrification process, has been confirmed through numerous ecological studies. Though newly available amoA (ammonia monooxygenase subunit A) gene sequences from new environments are accumulating rapidly in public repositories, a lack of information on the ecological and evolutionary factors shaping community assembly of AOA on the global scale is apparent. Methodology and Results We conducted a meta-analysis on uncultured AOA using over ca. 6,200 archaeal amoA gene sequences, so as to reveal their community distribution patterns along a wide spectrum of physicochemical conditions and habitat types. The sequences were dereplicated at 95% identity level resulting in a dataset containing 1,476 archaeal amoA gene sequences from eight habitat types: namely soil, freshwater, freshwater sediment, estuarine sediment, marine water, marine sediment, geothermal system, and symbiosis. The updated comprehensive amoA phylogeny was composed of three major monophyletic clusters (i.e. Nitrosopumilus, Nitrosotalea, Nitrosocaldus) and a non-monophyletic cluster constituted mostly by soil and sediment sequences that we named Nitrososphaera. Diversity measurements indicated that marine and estuarine sediments as well as symbionts might be the largest reservoirs of AOA diversity. Phylogenetic analyses were further carried out using macroevolutionary analyses to explore the diversification pattern and rates of nitrifying archaea. In contrast to other habitats that displayed constant diversification rates, marine planktonic AOA interestingly exhibit a very recent and accelerating diversification rate congruent with the lowest phylogenetic diversity observed in their habitats. This result suggested the existence of AOA communities with different evolutionary history in the different habitats. Conclusion and Significance Based on an up-to-date amoA phylogeny, this analysis provided insights into the possible evolutionary mechanisms and environmental parameters that shape AOA community assembly at global scale.
Merged Switch Allocation and Traversal in Network-on-Chip Switches

Large systems-on-chip (SoCs) and chip multiprocessors (CMPs), incorporating tens to hundreds of cores, create a significant integration challenge. Interconnecting a huge amount of architectural modules in an efficient manner, calls for scalable solutions that would offer both high throughput and low-latency communication. The switches are the basic building blocks of such interconnection networks and their design critically affects the performance of the whole system. So far, innovation in switch design relied mostly to architecture-level solutions that took for granted the characteristics of the main building blocks of the switch, such as the buffers, the routing logic, the arbiters, the crossbar's multiplexers, and without any further modifications, tried to reorganize them in a more efficient way. Although such pure high-level design has produced highly efficient switches, the question of how much better the switch would be if better building blocks were available remains to be investigated. In this paper, we try to partially answer this question by explicitly targeting the design from scratch of new soft macros that can handle concurrently arbitration and multiplexing and can be parameterized with the number of inputs, the data width, and the priority selection policy. With the proposed macros, switch allocation, which employs either standard round robin or more sophisticated arbitration policies with significant network-throughput benefits, and switch traversal, can be performed simultaneously in the same cycle, while still offering energy-delay efficient implementations.
Antioxidant supplements and semen parameters: An evidence based review

Many studies have focused on male infertility. There is limited evidence about the influence of nutrition on quality of semen. Approximately, 30-80% of infertility cases are caused by oxidative stress and decreased level of seminal total antioxidant capacity. This study was aimed to review the effects of oral antioxidant supplements on improving major semen parameters such as sperm concentration, motility, morphology, DNA damage, and fertility rate. Data were extracted from PubMed and Google scholar database by using the terms “antioxidant”, “multivitamin”, “carnitine”, “CoQ10”, “vitamin C”, “vitamin E”, “zinc”, “folic acid”, “N-acetyl cysteine” and “selenium” combined with “male infertility”, “semen”, and “sperm” to generate a set of relevant citations. Supplements such as CoQ10 and alpha-tocopherol significantly improve sperm count. Also, carnitine has positive effects on sperm motility and morphology. Simultaneous administration of vitamin E and vitamin C reduces the sperm DNA damage. However, in some studies, one or more factors have not changed substantially. In most of the studies, antioxidant supplementation improved the number, motility, morphology and sometimes DNA integrity of sperm. The present study showed that antioxidant supplements, especially a combination of antioxidants such as vitamin C, vitamin E, and CoQ10 intake can effectively improve semen parameters in infertile men.
Device Parameter Optimization of Silicon Germanium HBT for THZ Applications

Nowadays SiGe HBTs are surpassing even the fastest III-V production devices in the high–speed orbit. The state-of-art in simulation of silicon germanium semiconductor devices is presented in this paper. A comprehensive course of action to model the device parameter characterization of High Frequency 0. 1μm SiGe HBT is depicted which is based on the technique of direct parameter extraction. With the help of S-, Y- and Z-parameters, the equivalent circuit parameters have been extracted in a faultless approach. The intrinsic and the extrinsic elements of model are obtained using a direct extraction method that assists to find out the base resistance from the Z-parameters. In this, the issues entailed in simultaneous optimization of fmax and fT and related optimization of base resistance as well as junction capacitance are addressed. The device characteristics of the SiGe HBT are found much advance to those of III-V semiconductor devices. A corroboration of objective validity of the modeling scheme and the extraction of parameter is accomplished in the form of S-parameters. These results have been validated using a viable numerical device simulator ATLAS from Silvaco International.
Respiratory Health Symptoms among Students Exposed to Different Levels of Air Pollution in a Turkish City

In this study, we aimed to investigate the frequency of respiratory health symptoms among high school students attending schools at industrial, urban and rural areas in a Turkish city. Three schools located in different zones of the city having different pollution characteristics were chosen based on the pollutant distribution maps using Geographical Information Systems (GIS) software. A cross-sectional survey was performed among 667 high school students in the schools. Outdoor and indoor nitrogen dioxide (NO2) and ozone (O3) concentrations were also measured by passive samplers in the same schools to investigate possible routes of exposure. Chronic pulmonary disease (OR = 1.49; 95%CI: 1.11–1.99; p = 0.008), tightness in the chest (OR = 1.57; 95%CI: 1.22–2.02; p = 0.001), morning cough (OR = 1.81 95%CI: 1.19–2.75; p = 0.006) were higher among students in the industrial zone where nitrogen dioxide and ozone levels were also highest. There were no indoor sources of nitrogen dioxide and ozone exists in the schools except for the dining hall. As a conclusion, this study has noticed that air pollution and respiratory health problems among high school students are high in industrial zones and the use of passive samplers combined with GIS is an effective tool that may be used by public health researchers to identify pollutant zones and persons at risk.