Miracle-dz/UniFAR-FTUs huggingface dataset:
enes for eucalyptus wood Note Genomics of Eucalyptus wood traits

A major focus of our research has been on using molecular technologies to guide breeding for high value wood and fibre traits in eucalypts. One approach has been to use genomic maps to locate and characterise QTL that control wood and fibre traits. A generic map for eucalypts has been developed that consists of codominant markers that can be assayed across the major commercial species. Also on the map are candidate genes for traits such as flowering and wood and fibre traits. QTL have been characterised for wood density, fibre length, pulp yield and microfibril angle. A number of these have been validated in a related pedigree. A subset of QTL colocates with candidate genes. Research is now focussed on DNA sequence variation in different parts of these candidate genes and determining if this variation is associated with variation in wood properties. Of particular interest are genes involved in fibre development and cell wall formation. A third approach is to profile the expression of genes in the tissue of interest and determine if this relates to variation in trait performance. Microarrays are being used to relate expression of several thousand genes in xylem tissue to variation in traits such as microfibril angle and density. eucalypt / linkage maps / QTL / candidate genes / xylem / microarrays Résumé – Génomique des critères de qualité du bois d’eucalyptus. Notre recherche a été concentrée sur l’utilisation de technologies moléculaires pour guider l’amélioration génétique de critères importants de la qualité du bois et des fibres. On a développé une carte générique pour les eucalyptus à partir de marqueurs co-dominants intéressant les principales espèces d’intérêt commercial. Figurent également sur cette carte des gènes candidats concernant des caractères tels que la floraison et la qualité du bois et des fibres. On a mis en évidence des QTL pour la densité du bois, la longueur des fibres, le rendement en pâte et l’angle des microfibrilles. Un certain nombre ont été validés sur des familles apparentées à généalogie connue. Un sous ensemble de QTL sont co-localisés avec des gènes candidats. On concentre maintenant les recherches sur la variabilité de séquences ADN de ces gènes candidats pour savoir si elle est associée à celle des critères de qualité du bois. Sont d’un intérêt particulier les gènes impliqués dans le développement des fibres et la formation des parois cellulaires. Une troisième approche consiste à profiler l’expression des gènes dans les tissus en cause et à rechercher s’il existe d’éventuelles relations avec la variabilité des caractères. On utilise des microréseaux pour relier l’expression de plusieurs milliers de gènes du xylème avec la variabilité de caractères tels que l’angle des microfibrilles et la densité du bois. eucalyptus / carte de liaison / QTL / gènes candidats / xylème / microréseaux
Most Likely Voronoi Diagrams in Higher Dimensions

The Most Likely Voronoi Diagram is a generalization of the well known Voronoi Diagrams to a stochastic setting, where a stochastic point is a point associated with a given probability of existence, and the cell for such a point is the set of points which would classify the given point as its most likely nearest neighbor. We investigate the complexity of this subdivision of space in d dimensions. We show that in the general case, the complexity of such a subdivision is Omega(n^{2d}) where n is the number of points. This settles an open question raised in a recent (ISAAC 2014) paper of Suri and Verbeek, which first defined the Most Likely Voronoi Diagram. We also show that when the probabilities are assigned using a random permutation of a fixed set of values, in expectation the complexity is only ~O(n^{ceil{d/2}}) where the ~O(*) means that logarithmic factors are suppressed. In the worst case, this bound is tight up to polylog factors.
Comparisons in Gender Wage Differentials and Discrimination between Germany and the United Kingdom

Due to the lack of consistent data, direct and robust comparisons of cross-country labour markets have been virtually impossible. This study uses a new panel data series that controls for inconsistencies, thus overcoming this problem. This study estimates gender wage differentials and gender discrimination in the German and United Kingdom labour markets. Panel estimates are used to identify general wage differences between the two countries, with cross-sectional comparisons undertaken to identify changes that have occurred between 1991 and 1993, that are consistent with known labour market policies. It is found that gender wage differentials are greater in the UK than Germany with employer discrimination against females attributed with the majority of the difference in both countries.
Person X Environment in the Peer Domain: Parenting Strategies and Preadolescent Physiological Responses in the Context of Peer Stress

ii Acknowledgments iv List of Tables vii List of Figures viii List of Abbreviations ix Chapter 1: Introduction 1 Chapter 2: Literature Review 6 Peer Relationships in Preadolescence: Developmental and Ecological Contexts 6 Parenting and Peer Adjustment 9 Parenting in the Peer Domain 10 Preadolescents’ Physiological Responses to Peer Stress 20 Person x Environment Interactions Predicting Peer Adjustment 25 Sex Differences in Peer Relationships and Parenting in the Peer Domain 32 The Present Study 34 Chapter 3: Method 39 Participants 39 Procedures 40 Measures 42 Plan of Analysis 48
Extracting Hyponymy Relations from Domain-Specific Free Texts

Domain-specific ontologies have shown their powerful usefulness in many application areas, such as semantic web, information sharing, and natural language processing. However, manually building of domain ontologies still remains a tedious and cumbersome task. Hyponymy is a core component of domain-specific ontologies. In this paper, we propose three symbolic learning methods, which are integrated together to extract hyponymies from un-annotated domain-specific Chinese free texts. The three symbolic learning methods include seed-driven learning, pattern-mediated learning, and term composition based learning. Experimental results show that the algorithm is adequate to extracting the hyponymies from unstructured domain-specific Chinese corpus.
Using Graph Summarization for Join-Ahead Pruning in a Distributed RDF Engine

The need for scalable and efficient RDF stores has seen a high demand recently. Many efficient systems, both centralized and distributed, have been proposed. Since a row-oriented output is required by SPARQL, most of the current systems rely on relational joins. One of the problems with relational joins, though, is a performance bottleneck imposed by the generation of large intermediate relations which could be avoided by using more accurate data and pruning statistics. To address this problem, recently several systems have been proposed that employ bisimulation-based graph summaries -- adopted from XML indexing -- over large RDF graphs in order to facilitate join-ahead pruning. In this paper, we discuss a different, locality-based, graph summarization approach for RDF data and highlight its utilization for join-ahead pruning in a distributed SPARQL engine. Based on our recently developed TriAD engine, we present a detailed comparison of processing techniques for these graph summaries over the synthetic LUBM benchmark.
Two-loop QCD gauge coupling at high temperatures

We determine the 2-loop effective gauge coupling of QCD at high temperatures, defined as a matching coefficient appearing in the dimensionally reduced effective field theory. The result allows to improve on one of the classic non-perturbative probes for the convergence of the weak-coupling expansion at high temperatures, the comparison of full and effective theory determinations of an observable called the spatial string tension. We find surprisingly good agreement almost down to the critical temperature of the deconfinement phase transition. We also determine one new contribution of order (g6T4) to the pressure of hot QCD.
Federal Reserve Bank of Minneapolis Research Department Staff Report 408 Liquidity in Asset Markets with Search Frictions *

We develop a search-theoretic model of financial intermediation and use it to study how trading frictions affect the distribution of asset holdings, asset prices, efficiency, and standard measures of liquidity. A distinctive feature of our theory is that it allows for unrestricted asset holdings, so market participants can accommodate trading frictions by adjusting their asset positions. We show that these individual responses of asset demands constitute a fundamental feature of illiquid markets: they are a key determinant of bid-ask spreads, trade volume, and trading delays–all the dimensions of market liquidity that search-based theories seek to explain. acknowledged. The views expressed herein are those of the authors and not necessarily those of the Federal Reserve Bank of Cleveland, the Federal Reserve Bank of Minneapolis, or the Federal Reserve System.
Ovarian morphology is a marker of heritable biochemical traits in sisters with polycystic ovaries.

CONTEXT Polycystic ovary syndrome (PCOS) is a common endocrinopathy of uncertain etiology but with strong evidence for a genetic contribution. OBJECTIVE The objective of the study was to test the hypothesis that the typical polycystic ovarian morphology is a marker of inherited biochemical features in families of women with PCOS. DESIGN A study of probands with PCOS and their sisters. PATIENTS Patients included 125 probands and 214 sisters. All probands had PCOS, defined by symptoms of anovulation and/or hyperandrogenism with polycystic ovaries on ultrasound. Affected sisters were defined by polycystic ovaries, regardless of symptoms, and unaffected sisters defined by normal ovarian morphology. SETTING This was a clinic-based study. MAIN OUTCOME MEASURES Clinical, endocrine, and metabolic features in the various groups were compared, and estimates of broad-sense heritability were obtained using the quantitative transmission disequilibrium test. RESULTS Although affected sisters had fewer symptoms than probands (30% had no symptoms of PCOS), serum testosterone, androstenedione, LH, and fasting insulin and insulin sensitivity were similar in the two groups with polycystic ovaries but significantly different from those in unaffected sisters or controls. We observed moderate to high heritabilities for all traits studied in affected sister pairs, whereas heritabilities calculated from discordant siblings were substantially lower. CONCLUSIONS These data provide further evidence for a genetic basis of PCOS. The high heritability of biochemical features in probands and affected sisters, despite wide variation in symptoms, shows that not only are these biochemical traits strongly influenced by genetic factors but also, importantly, that polycystic ovarian morphology is an index of inherited traits in families with PCOS.
Discharge Ignition Near a Dielectric

Electrical breakdown in noble gas near a dielectric is an important issue in lighting industry. In order to investigate the influence of the dielectric on the ignition process, we perform measurements in argon, with pressure varying from 0.1 to 1 bar, using a pin-pin electrode geometry. Here, we present time-resolved images of ignition process for two different distances from electrodes to the dielectric.
Circulating microRNAs as stable blood-based markers for cancer detection

Improved approaches for the detection of common epithelial malignancies are urgently needed to reduce the worldwide morbidity and mortality caused by cancer. MicroRNAs (miRNAs) are small (≈22 nt) regulatory RNAs that are frequently dysregulated in cancer and have shown promise as tissue-based markers for cancer classification and prognostication. We show here that miRNAs are present in human plasma in a remarkably stable form that is protected from endogenous RNase activity. miRNAs originating from human prostate cancer xenografts enter the circulation, are readily measured in plasma, and can robustly distinguish xenografted mice from controls. This concept extends to cancer in humans, where serum levels of miR-141 (a miRNA expressed in prostate cancer) can distinguish patients with prostate cancer from healthy controls. Our results establish the measurement of tumor-derived miRNAs in serum or plasma as an important approach for the blood-based detection of human cancer.
One-carbon genetic variants and the role of MTHFD1 1958G>A in liver and colon cancer risk according to global DNA methylation

Several polymorphic gene variants within one-carbon metabolism, an essential pathway for nucleotide synthesis and methylation reactions, are related to cancer risk. An aberrant DNA methylation is a common feature in cancer but whether the link between one-carbon metabolism variants and cancer occurs through an altered DNA methylation is yet unclear. Aims of the study were to evaluate the frequency of one-carbon metabolism gene variants in hepatocellular-carcinoma, cholangiocarcinoma and colon cancer, and their relationship to cancer risk together with global DNA methylation status. Genotyping for BHMT 716A>G, DHFR 19bp ins/del, MTHFD1 1958G>A, MTHFR 677C>T, MTR 2756A>G, MTRR 66A>G, RFC1 80G>A, SHMT1 1420C>T, TCII 776C>G and TS 2rpt-3rpt was performed in 102 cancer patients and 363 cancer-free subjects. Methylcytosine (mCyt) content was measured by LC/MS/MS in peripheral blood mononuclear cells (PBMCs) DNA. The MTHFD1 1958AA genotype was significantly less frequent among cancer patients as compared to controls (p = 0.007) and related to 63% reduction of overall cancer risk (p = 0.003) and 75% of colon cancer risk (p = 0.006). When considering PBMCs mCyt content, carriers of the MTHFD1 1958GG genotype showed a lower DNA methylation as compared to carriers of the A allele (p = 0.048). No differences were highlighted by evaluating a possible relationship between the other polymorphisms analyzed with cancer risk and DNA methylation. The MTHFD1 1958AA genotype is linked to a significantly reduced cancer risk. The 1958GG genotype is associated to PBMCs DNA hypomethylation as compared to the A allele carriership that may exert a protective effect for cancer risk by preserving from DNA hypomethylation.
Compact analog counting SPAD pixel with 1.9% PRNU and 530ps time gating

In this paper, a pixel for time-resolved single photon detection is presented. The pixel includes a passively quenched Single-Photon Avalanche Diode (SPAD), a gating circuit and an analog counter based on charge sharing approach. The analog output signal delivered by the pixel is quantized in discrete levels, corresponding to different photon counts. Three linear arrays with different pixel versions were fabricated in a standard 0. 15μm CMOS technology. The electro-optical characterization demonstrated a counter non-uniformity of 1.1% and a Photo-Response Non-Uniformity (PRNU) of 1.9%, including SPAD non-uniformity. The pixel exhibits shot-noise limited operation and a minimum gating window width of 530ps FWHM.
Effects of Methanogenic Inhibitors on Methane Production and Abundances of Methanogens and Cellulolytic Bacteria in In Vitro Ruminal Cultures

ABSTRACT The objective of this study was to systematically evaluate and compare the effects of select antimethanogen compounds on methane production, feed digestion and fermentation, and populations of ruminal bacteria and methanogens using in vitro cultures. Seven compounds, including 2-bromoethanesulphonate (BES), propynoic acid (PA), nitroethane (NE), ethyl trans-2-butenoate (ETB), 2-nitroethanol (2NEOH), sodium nitrate (SN), and ethyl-2-butynote (EB), were tested at a final concentration of 12 mM. Ground alfalfa hay was included as the only substrate to simulate daily forage intake. Compared to no-inhibitor controls, PA, 2NEOH, and SN greatly reduced the production of methane (70 to 99%), volatile fatty acids (VFAs; 46 to 66%), acetate (30 to 60%), and propionate (79 to 82%), with 2NEOH reducing the most. EB reduced methane production by 23% without a significant effect on total VFAs, acetate, or propionate. BES significantly reduced the propionate concentration but not the production of methane, total VFAs, or acetate. ETB or NE had no significant effect on any of the above-mentioned measurements. Specific quantitative-PCR (qPCR) assays showed that none of the inhibitors significantly affected total bacterial populations but that they did reduce the Fibrobacter succinogenes population. SN reduced the Ruminococcus albus population, while PA and 2NEOH increased the populations of both R. albus and Ruminococcus flavefaciens. Archaeon-specific PCR-denaturing gradient gel electrophoresis (DGGE) showed that all the inhibitors affected the methanogen population structure, while archaeon-specific qPCR revealed a significant decrease in methanogen population in all treatments. These results showed that EB, ETB, NE, and BES can effectively reduce the total population of methanogens but that they reduce methane production to a lesser extent. The results may guide future in vivo studies to develop effective mitigation of methane emission from ruminants.
Feeder-free derivation of induced pluripotent stem cells from adult human adipose stem cells

Ectopic expression of transcription factors can reprogram somatic cells to a pluripotent state. However, most of the studies used skin fibroblasts as the starting population for reprogramming, which usually take weeks for expansion from a single biopsy. We show here that induced pluripotent stem (iPS) cells can be generated from adult human adipose stem cells (hASCs) freshly isolated from patients. Furthermore, iPS cells can be readily derived from adult hASCs in a feeder-free condition, thereby eliminating potential variability caused by using feeder cells. hASCs can be safely and readily isolated from adult humans in large quantities without extended time for expansion, are easy to maintain in culture, and therefore represent an ideal autologous source of cells for generating individual-specific iPS cells.
Membrane Fusion Intermediates via Directional and Full Assembly of the SNARE Complex

No More Fusion Confusion Biophysical models explain membrane fusion as a sequence of steps—including membrane contact, formation of a fusion stalk (merger of proximal monolayers), development of contact between distal monolayers that may or may not expand (hemifusion), and, finally, rupture of this diaphragm resulting in the opening of a fusion pore. Biological membrane fusion reactions are often driven by so-called SNARE proteins. By using a reconstituted membrane fusion system, Hernandez et al. (p. 1581, published online 31 May) have now been able to correlate precisely the states of SNARE zippering with intermediate structures along the fusion pathway. The results suggest that a tightly docked state, with a membrane distance so close that no proteins fit in between them, represents a critical fusion intermediate as a consequence of SNARE zippering. This intermediate is incompatible with a SNARE-driven stalk or with a ringlike arrangement of SNAREs depicted in most current models of membrane fusion. During vesicle membrane fusion, straining of lipids at the edges of an extended contact zone may initiate fusion. Cellular membrane fusion is thought to proceed through intermediates including docking of apposed lipid bilayers, merging of proximal leaflets to form a hemifusion diaphragm, and fusion pore opening. A membrane-bridging four-helix complex of soluble N-ethylmaleimide–sensitive factor attachment protein receptors (SNAREs) mediates fusion. However, how assembly of the SNARE complex generates docking and other fusion intermediates is unknown. Using a cell-free reaction, we identified intermediates visually and then arrested the SNARE fusion machinery when fusion was about to begin. Partial and directional assembly of SNAREs tightly docked bilayers, but efficient fusion and an extended form of hemifusion required assembly beyond the core complex to the membrane-connecting linkers. We propose that straining of lipids at the edges of an extended docking zone initiates fusion.
Resistance of human cervical carcinoma cells to tumor necrosis factor correlates with their increased sensitivity to cisplatin: evidence of a role for DNA repair and epidermal growth factor receptor.

Alterations in cellular biochemistry which are associated with the development of resistance to cytotoxic peptides, such as tumor necrosis factor (TNF), may also be responsible for changes in the response of cells to cytotoxic agents. Culturing ME-180 cervical carcinoma cells in the presence of escalating concentrations of TNF resulted in the development of an ME-180 cell variant (ME-180R) resistant to TNF but expressing a 3-5-fold increased sensitivity to cisplatin (CDDP) when measured following continuous exposure (low doses) or short-term incubation with CDDP (high doses) and clonogenic analysis. Cellular platinum uptake, efflux, and nuclear platinum content as well as the extent of DNA platination were examined and found to be identical in both ME-180 parental and ME-180R cell lines. Although ME-180R cells showed a relatively higher glutathione content than ME-180 parental cells, the effect of buthionine sulfoximine on the cellular sensitivity to CDDP and glutathione S-transferase activities of both cell lines were almost identical, suggesting that glutathione content or its metabolism did not appear to play a major role in differential CDDP cytotoxicity. Unscheduled DNA synthesis following exposure to CDDP was more inducible in ME-180 parental cells than in CDDP-sensitive ME-180R cells. Alkaline elution studies of cross-linked DNA in CDDP-treated ME-180 cells suggested that accumulation of DNA adducts reached maximal levels 10-15 h after CDDP treatment and was similar in both TNF-resistant and parental cells. Within 24 h after CDDP exposure, the extent of DNA cross-linking was markedly reduced in parental cells but remained elevated in the CDDP-sensitive ME-180R cell line. To examine the proposed regulatory role of phosphorylation in CDDP and TNF-mediated cytotoxicity, epidermal growth factor (EGF) receptor tyrosine kinase activity was measured in both TNF-resistant and parental ME-180 cells. Analysis of cell lysates demonstrated a 3-4-fold higher EGF receptor tyrosine kinase activity in ME-180R cells when compared to the parental population which correlated with increased expression of EGF receptor protein by immunoblot analysis. Based upon colony-forming assays, EGF treatment of ME-180 parental cells resulted in an increased sensitivity to CDDP (similar to ME-180R cells) and 3-fold stimulation of EGF receptor tyrosine kinase activity. Taken together, these results suggest that TNF resistance in ME-180 cervical carcinoma cells correlates with both increased EGF receptor expression and enhanced CDDP cytotoxicity. (ABSTRACT TRUNCATED AT 400 WORDS)