Miracle-dz/UniFAR-FTUs huggingface dataset:
The Arabidopsis YUCCA1 Flavin Monooxygenase Functions in the Indole-3-Pyruvic Acid Branch of Auxin Biosynthesis[W]

The flavin monooxygenase YUC1 and the Trp aminotransferase TAA1 were previously believed to function in two independent auxin biosynthetic pathways. The genetic and biochemical evidence presented herein demonstrates that the YUC1 and TAA1 gene families work in a single route, providing a new simplified view of how auxin is produced in plants. The effects of auxins on plant growth and development have been known for more than 100 years, yet our understanding of how plants synthesize this essential plant hormone is still fragmentary at best. Gene loss- and gain-of-function studies have conclusively implicated three gene families, CYTOCHROME P450 79B2/B3 (CYP79B2/B3), YUCCA (YUC), and TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS1/TRYPTOPHAN AMINOTRANSFERASE-RELATED (TAA1/TAR), in the production of this hormone in the reference plant Arabidopsis thaliana. Each of these three gene families is believed to represent independent routes of auxin biosynthesis. Using a combination of pharmacological, genetic, and biochemical approaches, we examined the possible relationships between the auxin biosynthetic pathways defined by these three gene families. Our findings clearly indicate that TAA1/TARs and YUCs function in a common linear biosynthetic pathway that is genetically distinct from the CYP79B2/B3 route. In the redefined TAA1-YUC auxin biosynthetic pathway, TAA1/TARs are required for the production of indole-3-pyruvic acid (IPyA) from Trp, whereas YUCs are likely to function downstream. These results, together with the extensive genetic analysis of four pyruvate decarboxylases, the putative downstream components of the TAA1 pathway, strongly suggest that the enzymatic reactions involved in indole-3-acetic acid (IAA) production via IPyA are different than those previously postulated, and a new and testable model for how IAA is produced in plants is needed.
A novel transgenic line using the Cre–lox system to allow permanent lineage‐labeling of the zebrafish neural crest

Accurate lineage tracing is crucial to understanding of developmental and stem cell biology, but is particularly challenging for transient and highly dispersive cell‐types like the neural crest (NC). The authors report in this article a new zebrafish transgenic line Tg(‐4725sox10:Cre)ba74. This line expresses Cre under the control of a well‐characterized portion of the sox10 promoter and, by crossing to a floxed‐reporter line, the authors show in this article that expression in this line is consistent with those described for GFP reporter lines using the same promoter. Reporter expression is readily detected in patterns consistent with the early expression domains. Thus, the authors see all major groups (pigment, neural, and skeletal) of NC‐derived cell‐types, as well as cell‐types derived from the known non‐NC sites of sox10 expression, including otic epithelium and oligodendrocytes. This line provides an invaluable tool for the further study of zebrafish NC development and NC‐derived stem cells as well as that of the otic vesicle and oligodendrocytes. genesis 50:750–757, 2012. © 2012 Wiley Periodicals, Inc.
On the Secure Degrees of Freedom of the K-user MAC and 2-user Interference Channels

We investigate the secure degrees of freedom (SDoF) of the K-user MIMO multiple access (MAC) and the two user MIMO interference channel. An unknown number of eavesdroppers are trying to decode the messages sent by the transmitters. Each eavesdropper is equipped with a number of antennas less than or equal to a known value NE. The legitimate transmitters and receivers are assumed to have global channel knowledge. We present the sum SDoF of the two user MIMO interference channel. We derive an upperbound on the sum SDoF of the K-user MAC channel and present an achievable scheme that partially meets the derived upperbound.
Regulation of Satellite Cell Function in Sarcopenia

The mechanisms contributing to sarcopenia include reduced satellite cell (myogenic stem cell) function that is impacted by the environment (niche) of these cells. Satellite cell function is affected by oxidative stress, which is elevated in aged muscles, and this along with changes in largely unknown systemic factors, likely contribute to the manner in which satellite cells respond to stressors such as exercise, disuse, or rehabilitation in sarcopenic muscles. Nutritional intervention provides one therapeutic strategy to improve the satellite cell niche and systemic factors, with the goal of improving satellite cell function in aging muscles. Although many elderly persons consume various nutraceuticals with the hope of improving health, most of these compounds have not been thoroughly tested, and the impacts that they might have on sarcopenia and satellite cell function are not clear. This review discusses data pertaining to the satellite cell responses and function in aging skeletal muscle, and the impact that three compounds: resveratrol, green tea catechins, and β-Hydroxy-β-methylbutyrate have on regulating satellite cell function and therefore contributing to reducing sarcopenia or improving muscle mass after disuse in aging. The data suggest that these nutraceutical compounds improve satellite cell function during rehabilitative loading in animal models of aging after disuse (i.e., muscle regeneration). While these compounds have not been rigorously tested in humans, the data from animal models of aging provide a strong basis for conducting additional focused work to determine if these or other nutraceuticals can offset the muscle losses, or improve regeneration in sarcopenic muscles of older humans via improving satellite cell function.
Complete nucleotide sequence of the Streptomyces lividans plasmid pIJ101 and correlation of the sequence with genetic properties

The complete nucleotide sequence of the multicopy Streptomyces plasmid pIJ101 has been determined and correlated with previously published genetic data. The circular DNA molecule is 8,830 nucleotides in length and has a G+C composition of 72.98%. The use of a computer program, FRAME, enabled identification in the sequence of seven open reading frames, four of which, tra (621 amino acids [aa]), spdA (146 aa), spdB (274 aa), and kilB (177 aa), appear to be genes involved in plasmid transfer. At least two of the above genes are predicted to be transcribed by known promoters that are regulated in trans by the products of the korA (241 aa) and korB (80 aa) loci on the plasmid. The segment of the plasmid capable of autonomous replication contains one large open reading frame (rep; 450 aa) and a noncoding region presumed to be the origin of replication. Four other small (less than 90 aa) open reading frames are also present on the plasmid, although no function can be attributed to them. The sequence of the pIJ101 replication segment present in several widely used cloning vectors (e.g., pIJ350 and pIJ702) has also been determined, so that the complete nucleotide sequences of these vectors are now known.
Age as a Modulator of Inflammatory Cardiovascular Risk Factors

Objective— Levels of acute phase reactants are affected by age. The extent to which cardiovascular risk associated with aging is due to an increase in the inflammatory burden is not known. We assessed the relationship with age of inflammatory markers, representing (1) systemic (C-reactive protein, fibrinogen, and serum amyloid-A) and (2) vascular (lipoprotein-associated phospholipase A2 and pentraxin-3) inflammation. Methods and Results— We determined lipoprotein-associated phospholipase A2 mass and activity, C-reactive protein, fibrinogen, serum amyloid-A, and pentraxin-3 levels and other cardiovascular disease risk factors in 336 whites and 224 African Americans. Levels of systemic inflammatory markers increased significantly with age in both ethnic groups (P<0.05 for all), whereas trend patterns of vascular inflammatory markers did not change significantly with age for either group. In multivariate regression models adjusting for confounding variables, age remained independently associated with a composite Z score for systemic but not vascular inflammation (&bgr;=0.250, P<0.001, and &bgr;=0.276, P<0.001, for whites and African Americans, respectively). Conclusion— We report an increase in the systemic but not vascular inflammatory burden with age. Levels of both categories of inflammatory markers with age were similar across ethnicity after adjustment for confounders. Our results underscore the importance of age in evaluating inflammatory markers to assess cardiovascular risk.
IGR J16194–2810: a new symbiotic X-ray binary

We here report on the multiwavelength study which led us to the identification of X-ray source IGR J16194-2810 as a new Symbiotic X-ray Binary (SyXB), that is, a rare type of Low Mass X-ray Binary (LMXB) composed of a M-type giant and a compact object. Using the accurate X-ray position allowed by Swift /XRT data, we pinpointed the optical counterpart, a M2 III star. Besides, the combined use of the spectral information afforded by XRT and INTEGRAL /IBIS shows that the 0.5-200 keV spectrum of this source can be described with an absorbed Comptonization model, usually found in LMXBs and, in particular, in SyXBs. No long-term (days to months) periodicities are detected in the IBIS data. The time coverage afforded by XRT reveals shot-noise variability typical of accreting Galactic X-ray sources, but is not good enough to explore the presence of X-ray short-term (seconds to hours) oscillations in detail. By using the above information, we infer important parameters for this source such as its distance (~3.7 kpc) and X-ray luminosity (~$1.4\times10^{35}$ erg s -1 in the 0.5-200 keV band), and we give a description for this system (typical of SyXBs) in which a compact object (possibly a neutron star) accretes from the wind of its M-type giant companion. We also draw some comparisons between IGR J16194-2810 and other sources belonging to this subclass, finding that this object resembles SyXBs 4U 1700+24 and 4U 1954+31.
Optimizing Cochlear Implant Speech Performance

Results of studies performed in our laboratory suggest that cochlear implant recipients understand speech best if the following speech processor parameters are individually chosen for each person: minimum and maximum stimulation levels on each electrode in the speech processor program (MAP), stimulation rate, and speech coding strategy. If these and related parameters are chosen to make soft sounds (from approximately 100 to 6,000 Hz) audible at as close to 20 dB hearing level as possible and loud sounds not too loud, recipients have the opportunity to hear speech in everyday life situations that are of key importance to children who are learning language and to all recipients in terms of ease of communication.
Sphere-packing bounds in the Grassmann and Stiefel manifolds

Applying the Riemann geometric machinery of volume estimates in terms of curvature, bounds for the minimal distance of packings/codes in the Grassmann and Stiefel manifolds will be derived and analyzed. In the context of space-time block codes this leads to a monotonically increasing minimal distance lower bound as a function of the block length. This advocates large block lengths for the code design
Scalable and elastic realtime click stream analysis using StreamMine3G

Click stream analysis is a common approach for analyzing customer behavior during the navigation through e-commerce or social network sites. Performing such an analysis in real-time opens up new business opportunities as well as increases revenues as recommendations can be generated on the fly making a previously unknown product to the potential customer attractive. As click streams are highly fluctuating as well as must be processed in real time, there is a high demand for Event-Stream-Processing (ESP) engines that are (1) horizontally as well as vertically scalable, (2) elastic in order to cope with the fluctuation in the data stream, and (3) provide efficient state management mechanisms in order to drive such kind of analysis. However, the majority of the nowadays ESP engines such as Apache S4 or Storm provide neither explicit state management nor techniques for elastic scaling. In this paper, we present StreamMine3G, a scalable and elastic ESP engine which provides state management out of the box, scales with the number of nodes as well as cores and improves performance due to a novel delegation mechanisms lowering contention on state as well as network links caused by fluctuations and temporary imbalances in the data streams.
Snowprofile measurements with a new method

Snow profile measurements in traditional way are time-consuming work. The excavation of a snow-pit, collecting measurements with several different instruments and writing a log of these values limits the amount of profiles that can be measured. The instrument concept presented here provides data with high vertical resolution without snow-pit excavations and very little disturbance to the natural state of the snow. These measurements take very little time making it possible to cover large geographical areas instead of a few selected snow-pit locations. The minimal disturbance caused provides a way to collect time-series of closely spaced profiles from snow in its natural state. This work presents the instrument concept and some early results on light extinction measurements with two incarnations of the protype instrument.
Explicit state model checking with generalized Büchi and Rabin automata

In the automata theoretic approach to explicit state LTL model checking, the synchronized product of the model and an automaton that represents the negated formula is checked for emptiness. In practice, a (transition-based generalized) Büchi automaton (TGBA) is used for this procedure. This paper investigates whether using a more general form of acceptance, namely transition-based generalized Rabin automata (TGRAs), improves the model checking procedure. TGRAs can have significantly fewer states than TGBAs, however the corresponding emptiness checking procedure is more involved. With recent advances in probabilistic model checking and LTL to TGRA translators, it is only natural to ask whether checking a TGRA directly is more advantageous in practice. We designed a multi-core TGRA checking algorithm and performed experiments on a subset of the models and formulas from the 2015 Model Checking Contest. We observed that our algorithm can be used to replace a TGBA checking algorithm without losing performance. In general, we found little to no improvement by checking TGRAs directly.
Social Selectivity in Adults' Novel Sound Learning

There is a good deal of evidence for the existence of social identity-based differences in speech (Labov 1972, and others), especially differences based on talker gender (Perry, Ohde, & Ashmead, 2001; Patterson & Werker, 2002; Foulkes, Docherty, & Watt 2005, and others). However, the nature of the process by which these differences are acquired is still unknown. The purpose of this study is to investigate sex-specific phonetic learning in a laboratory-based novel-sound learning task. Specifically, we examined male and female participants' tendencies to emulate phonetically distinct variants of novel sounds produced by talkers who shared their biological sex, as opposed to the variant produced by the opposite sex. We believe that the outcome of this endeavor will be a better understanding of how these variables might be acquired during first-language acquisition. To examine this, we created one set of one-syllable nonwords whose onsets contained a voiceless lateral obstruent, and another set whose onsets contained a velar fricative. These non-English sounds were used in order to control for any previous sex-related biases people may have for familiar English sounds. Audio productions of these novel words were recorded by two trained linguists whose voices the authors judged as being prototypically female and male. The novel words were presented one at a time, by either the female voice or the male voice, and were associated with novel objects shown on a computer screen. Each participant was trained on one onset which the man and woman produced differently (hereafter called “sexbiased”), and one onset which they produced equally variably (hereafter called “random”). The two variants for the voiceless lateral obstruent were the voiceless lateral fricative [ɬ] and the voiceless lateral affricate [tɬ]. The two variants for the velar fricative were the voiced velar fricative [ɣ] and the voiceless velar fricative [x]. Participants were systematically exposed to variations of onsets: half the participants heard sex-biased variation for the lateral onset and random variation for the velar onset, while the other half heard random variation for the lateral onset and sex-biased variation for the velar onset. Three iterations of learning phases followed by test phases were presented to each participant, first for one onset, then for the other. During the learning phases, participants saw a novel object on the screen and heard over headphones “This object is a ____”, spoken by either the man or the woman, and onsets varied accordingly. During the test phases, participants were asked to name objects whose pictures appeared on the screen one at a time. Below is the counter-balancing scheme used to systematically expose participants to both sex-biased and random variation. There were five women and five men in each of four groups.
Immediate and long-term functional impact of repetitive locomotor training as an adjunct to conventional physiotherapy for non-ambulatory patients after stroke

Purpose. The aim of the present study was to assess the heart rate intensity during gait training and to evaluate the relationship between heart rate intensity during gait training and walking ability of patients after stroke. Methods. We included non-ambulatory patients within six weeks after first stroke. Over four weeks patients were trained five times a week, with either 20 minutes of repetitive locomotor training and 25 min of physiotherapy (RLT-PT), or 45 min of PT alone. We assessed the heart rate intensity during training period. Additionally we assessed walking ability (Functional Ambulation Categories) and the rate of independent ability to perform activities of daily life (Barthel Index) at the end of study and six months and three years later on. Results. We included 30 patients in each group. Patients in RLT-PT group exercised longer in the HR target zone than in the PT group (16.1 ± 11.8 min vs. 5.3 ± 5.6 min, p < 0.001). Higher heart rates were associated with independent walking at the end of study, at six months and at three years after the end of study (Fishers exact test, p = 0.014, p = 0.012 and p = 0.017, respectively). Conclusions. Higher heart rate intensities during gait-training of non-ambulatory post-stroke patients may improve walking function.
The Two Ways of Assessing Heat-Related Mortality and Vulnerability.

In light of increasing recent media attention on climate change and global warming, heat-related mortality has become a much more visible public health concern. In the United States, heat is responsible for more fatal events than all other weather events combined. (1) Investigating and quantifying heat-related mortality has been done through two very different approaches. (Am J Public Health. Published online ahead of print September 17, 2015: e1-e2. doi:10.2105/AJPH.2015.302848). Language: en
Opposite re-ranking based on relevant sub-topic dispelling

Opposite re-ranking is a novel strategy to personalized information retrieval, it utilizes the description structure opposed to query intention, to achieve the recognition and dispelling of obstinate-negative feedback. At present, an important problem of the research in the opposite re-ranking is how to establish the maximum discriminative and representative opposite query intention. Aiming at the problem, this paper proposes an opposite re-ranking method based on dispelling of the relevant subtopics for the optimization of result list. The experiment makes use of TDT4 corpora to test, the results present this approach improves the search performance dramatically, the MAP enhances by 16 percents, P@20 and NDCG@20 increases by 14 percents and 12 percents respectively.
Acute renal insufficiency during telavancin therapy in clinical practice.

OBJECTIVES To describe the tolerance to long-term telavancin therapy among inpatients as it relates to nephrotoxicity. METHODS Retrospective cohort study of adult patients who received telavancin at the Barnes-Jewish Hospital from 1 September 2009 to 1 December 2010. Patients who received less than three doses of telavancin, were on haemodialysis prior to telavancin administration or died within 48 h of initial telavancin administration were excluded. RESULTS Twenty-one patients received telavancin and met the inclusion criteria. Seven of 21 patients (33%) developed acute renal insufficiency during therapy. Patients who developed acute renal insufficiency had a mean glomerular filtration rate reduction of 56 mL/min/1.73 m(2). In the univariate analysis, high body mass index (P=0.025), use of intravenous contrast dye (P=0.017) and prior serum vancomycin trough levels >20 mg/L (P=0.017) were associated with developing acute renal insufficiency. Two patients required haemodialysis; two had persistent renal insufficiency. CONCLUSIONS Supratherapeutic vancomycin trough levels, high body mass index and receipt of intravenous contrast dye prior to telavancin therapy were associated with acute renal insufficiency.
Sexual strategies theory: Historical origins and current status

In sexually reproducing organisms, no domain is more closely linked with the engine of the evolutionary process than sexuality. Men and women over human evolutionary history have confronted different adaptive problems in the sexual domain. Sexual Strategies Theory offers an account of these adaptive problems and presents a view of human sexual psychology as a rich repertoire of mechanisms that have evolved as adaptive solutions. A host of specific predictions about human sexuality follows from this analysis, including an account of sex differences in the desire for sexual variety, the qualities preferred in short‐term and long‐term mates, context‐dependent shifts in mate preferences, the nature of sexual jealousy, the tactics that are effective for attracting and retaining a mate, and the causes of sexual conflict between men and women. After reviewing the theory's historical origins, I summarize a portion of the extensive empirical research designed to test its tenets. An evaluation of the theory notes i.
Dendritic Cells and B Cells: Unexpected Partners in Th2 Development

Although we have known for decades that B cells contribute to immune responses by secreting Ab, it is now clear that they are more than simply factories for Ig production, and they also play key roles as modulators of T cell–dependent immunity. Indeed, the evidence showing that Ag-presenting and cytokine-producing B cells can alter the magnitude and quality of CD4 T cell responses continues to grow. In this article, we review the data showing that B cells, working in partnership with dendritic cells, regulate the development of Th2 cells and the subsequent allergic response.
Using Distance Estimates in Heuristic Search

This paper explores the use of an oft-ignored information source in heuristic search: a search-distance-to-go estimate. Operators frequently have different costs and cost-to-go is not the same as search-distance-to-go. We evaluate two previous proposals: dynamically weighted A* and A* epsilon. We present a revision to dynamically weighted A* that improves its performance substantially in domains where the search does not progress uniformly towards solutions, and particularly in certain temporal planning problems. We show how to incorporate distance estimates into weighted A* and improve its performance in several domains. Both approaches lead to dramatic performance increases in popular benchmark domains.