Miracle-dz/UniFAR-FTUs huggingface dataset:
Overexpression of a pH-sensitive nitrate transporter in rice increases crop yields

Significance Significant progress has been made in our understanding of plant adaptive responses to maintain cellular pH under varied N supply forms. Rice is a plant adapted to grow in waterlogged or dryland environments, in contrast to other crops, such as wheat, soybean, and maize. The nitrate transporter OsNRT2.3b provides a molecular mechanism explaining plant adaptation to the ammonium-nitrate supply shift between the waterlogged and drained soil environments. The sensing of cytosolic pH by OsNRT2.3b can function to improve rice nitrogen use efficiency and pH balance, providing an explanation for plant adaptation to changes in the form of N supply. Cellular pH homeostasis is fundamental for life, and all cells adapt to maintain this balance. In plants, the chemical form of nitrogen supply, nitrate and ammonium, is one of the cellular pH dominators. We report that the rice nitrate transporter OsNRT2.3 is transcribed into two spliced isoforms with a natural variation in expression ratio. One splice form, OsNRT2.3b is located on the plasma membrane, is expressed mainly in the phloem, and has a regulatory motif on the cytosolic side that acts to switch nitrate transport activity on or off by a pH-sensing mechanism. High OsNRT2.3b expression in rice enhances the pH-buffering capacity of the plant, increasing N, Fe, and P uptake. In field trials, increased expression of OsNRT2.3b improved grain yield and nitrogen use efficiency (NUE) by 40%. These results indicate that pH sensing by the rice nitrate transporter OsNRT2.3b is important for plant adaption to varied N supply forms and can provide a target for improving NUE.
Listening for Large Whales in the Offshore Waters of Alaska

January 2006 / Vol. 56 No. 1 • BioScience 49 L whales were severely depleted by commercial whaling from the 18th through the late 20th century, to such an extent that all were included in the initial US listing of endangered species in 1973. Targeted species included blue, fin, humpback, right, Bryde’s, and sperm whales (box 1), and although precise numbers are unknown, the removal of at least two million whales over roughly 200 years is well documented (Clapham et al. 1999). While this intensive exploitation underlies the recent controversial hypothesis of topdown ecosystem forcing—the so-called “megafaunal collapse” hypothesis (Springer et al. 2003, Mizroch and Rice forthcoming)—it also sets a challenge to scientists and resource managers charged with estimating current population sizes and habitat protection for these endangered species. With the end of the cold war and the subsequent willingness of the US government to allow dual use of some military assets (Nishimura and Conlon 1993), a unique opportunity arose to use the US Navy’s SOSUS (Sound Surveillance System) underwater hydrophone network to detect and track whales. Biologists welcomed this opportunity, and found in SOSUS an unprecedented tool to detect blue and fin whale calls over long distances in the North Atlantic and North Pacific basins (Clark 1995, Watkins et al. 2000, Stafford et al. 2001) and to track individual whales that produced atypical calls (Watkins et al. 2004). In the North Pacific, the seasonal detection of endangered blue and fin whale calls, using SOSUS, provided a means to correlate call occurrence with habitat features in remote areas off the Kamchatka Peninsula (Moore et al. 2002) and to investigate whale response to ocean climate variability off California (Burtenshaw et al. 2004). The success of research that used SOSUS to track seasonal occurrence patterns in whale calls fostered the development of autonomous recorders that could be deployed virtually anywhere in the world’s oceans (Fox et al. 2001, Wiggins 2003). Two types of recorders have been used off Alaska: (1) autonomous hydrophones developed by the National Oceanic and Atmospheric Administration’s (NOAA) Pacific Marine Environmental Laboratory (PMEL) (Fox et al. 2001; www. pmel.noaa.gov/vents/acoustics/whales/bioacoustics.html) and (2) acoustic recording packages (ARPs; Wiggins 2003, http:// cetus.ucsd.edu). The PMEL hydrophone consists of a watertight titanium pressure case containing alkaline batteries, a data logging system with one to six hard disk drives, and a hydrophone outside the case. The ARPs, developed by the Marine Physical Laboratory of the Scripps Institution of Oceanography, consist of a frame that holds the batteries, hard disk drives, and ballast, with a hydrophone suspended about 7 meters (m) above the frame. The recording bandwidth for both recorders ranges from 230 to 880 hertz (Hz) (sample rates 500 to 2000 Hz) depending on the unit, with hard disk drive storage capacity of 36 to 160 gigabytes. They are thus capa-
Isolation and characterization of new polymorphic simple sequence repeat loci in grape (Vitis vinifera L.).

Four new simple sequence repeat (SSR) loci (designated VVMD5, VVMD6, VVMD7, and VVMD8) were characterized in grape and analyzed by silver staining in 77 cultivars of Vitis vinifera. Amplification products ranged in size from 141 to 263 base pairs (bp). The number of alleles observed per locus ranged from 5 to 11 and the number of diploid genotypes per locus ranged from 13 to 27. At each locus at least 75% of the cultivars were heterozygous. Alleles differing in length by only 1 bp could be distinguished by silver staining, and size estimates were within 1 or 2 bp, depending on the locus, of those obtained by fluorescence detection at previously reported loci. Allele frequencies were generally similar in wine grapes and table grapes, with some exceptions. Some alleles were found only in one of the two groups of cultivars. All 77 cultivars were distinguished by the four loci with the exception of four wine grapes considered to be somatic variants of the same cultivar, 'Pinot noir', 'Pinot gris', 'Pinot blanc', and 'Meunier'; two table grapes that are known to be synonymous, 'Keshmesh' and 'Thompson Seedless'; and three table grapes, 'Dattier', 'Rhazaki Arhanon', and 'Markandi', the first two of which have been suggested to be synonymous. Although the high polymorphism at grape SSR loci suggests that very few loci would theoretically be needed to separate all cultivars, the economic and legal significance of grape variety identification requires the increased resolution that can be provided by a larger number of loci. The ease with which SSR markers and data can be shared internationally should encourage their broad use, which will in turn increase the power of these markers for both identification and genetic analysis of grape. Key words : grape, Vitis, microsatellite, simple sequence repeat, DNA typing, identification.
Analysis and Design of a Deep Subsurface Dam

107602-03-5353-IJCEE-IJENS © June 2010 IJENS I J E N S  Abstract— A 3-D finite element (FE) numerical model was used to analyze structurally a proposed subsurface concrete dam to serve as a strategic water supply storage for the Holy city of Makkah, Saudi Arabia. The work was done mainly to show the behavior of the subsurface dam under the subjecting loads. The plastic concrete was chosen for the construction of the cut-off wall required for the reservoir. Three-dimensional finite element analyses were made for three thicknesses of the cut-off walls: 0.6 to 0.8 m, 0.8 to 1.0 m and 1.0 to 1.2 m for the alluvium depths of 30, 50 and 70 m, respectively. The change in soil rigidity with depth was taken into account. The vertical and horizontal boundary conditions were designed to simulate the proper behavior of the structure It was found that increasing the thickness of the wall improves the distribution of the mobilized passive pressure opposite to the water pressure acting on the upstream face of the cut-off wall, while, the vertical and horizontal stresses developed in the wall due to the applied loads increased. In addition, stresses in the wall increase incrementally with the increase of wall height. The maximum horizontal and vertical stresses developed in proportion to the 1/6 bottom height of the wall. In the lower part of the wall, the mix with rich cement content must be used. It is recommended also to use vertical reinforcement imbedded by the anchorage length in the lock of the wall inside the bedrock and extended 1/20 the wall height. Results showed that the two vertical boundaries in the FE mesh must be placed at minimum distance equaling twice the height of the alluvium deposits from the centerline of the cut-off wall.
Overcoming Structural Resistance in SPI with Change Management

SPI initiatives can be seen as change programmes. Previous work has identified that such programmes are subject to resistance. A key challenge in the area is to understand the political issues in SPI change. However, at present there is little existing work in SPI related to the politics of improving. By adopting a view of politics as central to contemporary organizations, this paper reviews how we might understand resistance, how and why resistance occurs, and the implications of resistance for SPI. We provide a more detailed understanding of change management models (Katter's 8 steps and Prosci's Change Management Model) and their use in addressing resistance in SPI. It is argued that change management models can be used to accommodate the human factor of change in SPI. The paper explains the activities that help the successes of SPI initiatives and their relationship with the change management models. This paper contributes a structured change management approach to address resistance. We show from our experience how these approaches have been applied.
A novel diagnostic test for prostate cancer emerges from the determination of alpha-methylacyl-coenzyme a racemase in prostatic secretions.

PURPOSE With the recent discovery that alpha-methlyacly-coenzyme A racemase (AMACR) is over expressed in a majority of prostate cancer (CaP) specimens we developed a novel polymerase chain reaction (PCR) based approach that would predict the presence of CaP from prostatic secretions. MATERIALS AND METHODS A total of 21 patients were enlisted in this study, including 10 with CaP, 2 with high grade PIN and 9 cancer-free individuals (7 healthy men and 2 with benign hyperplasia). Total cellular RNA was extracted from prostatic secretions obtained from post-massage urine specimens. Levels of AMCAR transcripts and prostate specific antigen (PSA) transcripts in these samples were determined by quantitative reverse transcriptase-PCR analyses. Relative AMACR value scores (RAVSs) were calculated by normalizing the AMACR transcript level to that of PSA for each sample and multiplying by 100. An experimentally defined diagnostic cutoff RAVS value was determined in the cancer-free control group. RESULTS Neither AMACR nor PSA mRNA levels were predictive of CaP when used alone. However, using RAVS values and imposing a diagnostic cutoff value of 2 SDs above the mean RAVS in the cancer-free control group all 9 (100%) cancer-free individuals, including those with benign prostatic hyperplasia, were below the cutoff and 7 of 10 (70%) with CaP had RAVS above the cutoff. Furthermore, 2 of the 3 false-negative cases showed clinically insignificant disease. The 2 patients with high grade PIN were above the cutoff in this test. CONCLUSIONS In this study the quantification of AMACR transcripts normalized to PSA transcripts in prostatic secretions was shown to be predictive of CaP. Therefore, our novel approach using quantitative reverse transcriptase-PCR to detect the AMACR-to-PSA transcript ratio shows promise as a noninvasive screening test for CaP. Furthermore, early results demonstrate a trend toward excluding patients with clinically insignificant disease that may not yet require aggressive treatment due to a low cancer burden.
Effects of Ultrasound as Visual Feedback of the Tongue on Generalization, Retention, and Acquisition in Speech Therapy for Rhotics

Purpose: The purpose of this study was to provide an initial comparison of exposure to ultrasound visual feedback of the tongue and no exposure to ultrasound in speech therapy for postvocalic rhotics (the /r/ family of sounds). Effects of the two treatments on acquisition, retention, and generalization were explored in participants ages 7-9. Methods: A single-subject randomized block design replicated across four participants was used. Each week for seven weeks, one session containing high frequency ultrasound use and one session containing no ultrasound use were randomly ordered. A Training Probe List and Generalization Probe List consisting of monosyllabic words, multisyllabic words, phrases, and short sentences were used to measure acquisition within each session as well as retention and generalization between two consecutive sessions. Data analyses included: (a) descriptive statistics to complement visual inspections of single-subject graphs, (b) effect size calculation, and (c) statistical results from a randomization test. Results: One participant showed a significant advantage for ultrasound sessions over no ultrasound sessions in acquisition scores; however, there were no differences between treatment conditions for any participants in generalization or retention. Conclusion: For some children, acquisition may be facilitated by ultrasound visual feedback. No evidence suggested that ultrasound visual feedback inhibited retention or generalization in speech tasks. As a whole, treatment was effective for 2 of the 4 participants when comparing pre/post generalization data. Future studies should focus on evaluating the effectiveness of ultrasound visual feedback therapy given a larger dose (i.e., treatment duration) and differing age groups. Effects of Ultrasound as Visual Feedback of the Tongue on Generalization, Retention, and Acquisition in Speech Therapy for Rhotics By Greta M. Sjolie B. A. Simpson College
Influence of age and aerobic fitness on the multifractal characteristics of electrocardiographic RR time-series

Multifractal properties of electrocardiographic inter-beat (RR) time-series offer insight into its long-term correlation structure, independently of RR variability. Here we quantify multifractal characteristics of RR data during 24-h diurnal-nocturnal activity in healthy participants. We tested the hypotheses that (1) age, gender and aerobic fitness influence RR multifractal properties, and that (2) these are influenced by circadian variation. Seventy adults (39 males) aged 19–58 years and of various fitness levels were monitored using 24-h ECG. Participants were dichotomized by median age and fitness for sub-group analysis. Gender and fitness were independent of age (p = 0.1, p > 0.5). Younger/older group ages were substantially different (p < 0.0005) and were independent of gender and fitness. Multifractality was quantified using the probability spectrum of Hölder exponents (h), from which modal h (h*) and the full-width and half-widths at half-maximum measures (FWHM, HWHM+, and HWHM−) were derived. FWHM decreased (p = 0.004) and h* increased (p = 0.011) in older people, indicating diminished long-range RR correlations and weaker anti-persistent behavior. Anti-persistent correlation (h*) was strongest in the youngest/fittest individuals and weakest in the oldest/least fit individuals (p = 0.015). Long-range correlation (HWHM+/FWHM) was strongest in the fittest males and weakest in the least fit females (p = 0.007–0.033). Multifractal RR characteristics in our healthy participants showed strong age-dependence, with diminished long-range anti-persistent correlation in older people. Circadian variation of these characteristics was influenced by fitness and gender: fitter males and females of all ages had the greatest degree of multifractality or long-range order. Multifractal characterization appears to be a useful method for exploring the physiological basis of long-term correlation structure in RR time-series as well as the benefits thereon of physical fitness training.
A Coding Scheme for Visible Light Communication With Wide Dimming Range

For visible light communications (VLCs), dimming support is desirable to provide variable levels of lighting brightness. When error correction coding schemes are used for VLC systems, different code rates should be employed according to target dimming levels. In this letter, we propose a coding scheme, which can provide a wide range of brightness and a simple encoding/decoding structure for all different rates by using a rate-compatible punctured code. Puncturing patterns having the minimum bit error rate are provided by computer search. The results show that the VLC system with the proposed coding scheme can achieve optimum performances as well as a precise dimming support.
NAC Family Proteins NARS1/NAC2 and NARS2/NAM in the Outer Integument Regulate Embryogenesis in Arabidopsis[W][OA]

Seed morphogenesis consists of embryogenesis and the development of maternal tissues such as the inner and outer integuments, both of which give rise to seed coats. We show that expression of chimeric repressors derived from NAC-REGULATED SEED MORPHOLOGY1 and -2 (NARS1 and NARS2, also known as NAC2 and NAM, respectively) caused aberrant seed shapes in Arabidopsis thaliana. Double knockout mutant nars1 nars2 exhibited abnormally shaped seeds; moreover, neither nars1 nor nars2 produced abnormal seeds, indicating that NARS1 and NARS2 redundantly regulate seed morphogenesis. Degeneration of the integuments in nars1 nars2 was markedly delayed, while that of the wild type occurred around the torpedo-shaped embryo stage. Additionally, nars1 nars2 showed a defect in embryogenesis: some nars1 nars2 embryos were developmentally arrested at the torpedo-shaped embryo stage. Unexpectedly, however, neither NARS1 nor NARS2 was expressed in the embryo at this stage, although they were found to be expressed in the outer integument. Wild-type pistils pollinated with nars1 nars2 pollen generated normal seeds, while the reverse crossing generated abnormal seeds. Taken together, these results indicate that NARS1 and NARS2 regulate embryogenesis by regulating the development and degeneration of ovule integuments. Our findings suggest that there is an intertissue communication between the embryo and the maternal integument.
The State Political Party and the Policy-Making Process

This research investigated the proposition that variation in the structure of the political party can account for variation in the type of policy produced. The conditions under which legislators of the governor's party supported his legislative requests in sixteen sessions chosen for different degrees of party cohesion were investigated. The findings indicate that there is very little correlation between the legislator's district primary or election competition and his support for the governor's requests. The Democratic governor is supported by legislators from the districts in which he himself has strong party support as measured by his primary vote. The Republican governor's support cannot be geographically located in this manner. With respect to socioeconomic legislation, the pattern of support for a successful governor does not depend upon socioeconomic variables within the legislators' districts, but if the governor cannot control his legislators, socioeconomic variables provide the major basis for the factions which develop.
Welcome to the Revolution: Integrative Biology and Assessing the Impact of Endocrine Disruptors on Environmental and Public Health1

Abstract Concern continues to grow over the negative impact of endocrine disrupting chemicals on environmental and public health. The number of identified endocrine disrupting chemicals is increasing, but biological endpoints, experimental design, and approaches for examining and assessing the impact of these chemicals are still debated. Although some workers consider endocrine disruption an “emerging science,” I argue here that it is equally, a “merging science” developing in the tradition of integrative biology. Understanding the impact of endocrine disruptors on humans and wildlife is an examination of “context dependent development” and one that Scott Gilbert predicted would require a “new synthesis” or a “revolution” in the biological sciences. Here, I use atrazine as an example to demonstrate the importance of an integrative approach in understanding endocrine disruptors. Atrazine is a potent endocrine disruptor that chemically castrates and feminizes amphibians and other wildlife. These effects are the result of the induction of aromatase, the enzyme that converts androgens to estrogens, and this mechanism has been confirmed in all vertebrate classes examined (fish, amphibians, reptiles, birds, and mammals, including humans). To truly assess the impact of atrazine on amphibians in the wild, diverse fields of study including endocrinology, developmental biology, molecular biology, cellular biology, ecology, and evolutionary biology need to be invoked. To understand fully the long-term impacts on the environment, meteorology, geology, hydrology, chemistry, statistics, mathematics and other disciplines well outside of the biological sciences are required.
A Preemption Algorithm for a Multitasking Environment on Dynamically Reconfigurable Processors

Task preemption is a critical mechanism for building an effective multi-tasking environment on dynamically reconfigurable processors. When a task is preempted, its necessary state information must be correctly preserved in order for the task to be resumed later. Not only do coarse-grained Dynamically Reconfigurable Processing Array (DRPAs) devices have different architectures using a variety of development tools, but the great amount of state data of hardware tasks executing on such devices are usually distributed on many different storage elements. To address these difficulties, this paper aims at studying a general method for capturing the state data of hardware tasks targeting coarse-grained DRPAs. Based on resource usage, algorithms for identifying preemption points and inserting preemption states subject to user-specified preemption latency are proposed. Moreover, a modification to automatically incorporate proposed steps into the system design flow is also discussed. The performance degradation caused by additional preemption states is minimized by allowing preemption only at predefined points where demanded resources are small. The evaluation result using a model based on NEC Electronics' DRP-1 shows that the proposed method can produce preemption points satisfying a given preemption latency with reasonable hardware overhead (from 6% to 15%).
Providing probabilistically-bounded approximate answers to non-holistic aggregate range queries in OLAP

A novel framework for providing probabilistically-bounded approximate answers to non-holistic aggregate range queries in OLAP is presented in this paper. Such a framework allows us to efficiently support OLAP applications, as answering queries is the main bottleneck for this kind of applications. To this end, scalability of the techniques and accuracy of the answers are recognized as important limitations of state-of-the-art approximate query answering proposals in OLAP. Specifically, this paper is focused on the latter limitation, whereas it refers to results presented in [9] for the first one. The KSyn synopsis data structure, which implements the guidelines of the proposed framework and overcomes the recognized limitations, is also presented and discussed in detail, along with a query-conscious error metrics-based storage space allocation scheme. Finally, encouraging preliminary experimental results stating the goodness of our proposal are presented and discussed.