Miracle-dz/UniFAR-FTUs huggingface dataset:
Mapping of adult plant resistance to net form of net blotch in three Australian barley populations

Net form of net blotch (NFNB), caused by Pyrenophora teres Drechs. f. teres Smedeg. , is a serious disease problem for the barley industry in Australia and other parts of the world. Three doubled haploid barley populations, Alexis/Sloop, WI2875-1/Alexis, and Arapiles/Franklin, were used to identify genes conferring adult plant resistance to NFNB in field trials. Quantitative trait loci (QTLs) identified were specific for adult plant resistance because seedlings of the parental lines were susceptible to the NFNB isolates used in this study. QTLs were identified on chromosomes 2H, 3H, 4H, and 7H in both the Alexis/Sloop and WI2875-1/Alexis populations and on chromosomes 1H, 2H, and 7H in the Arapiles/Franklin population. Using QTLNetwork, epistatic interactions were identified between loci on chromosomes 3H and 6H in the Alexis/Sloop population, between 2H and 4H in the WI2875-1/Alexis population, and between 5H and 7H in the Arapiles/Franklin population. Comparisons with earlier studies of NFNB resistance indicate the pathotype-dependent nature of many resistance QTLs and the importance of establishing an international system of pathotype nomenclature and differential testing.
Determination of the mechanical medial proximal tibial angle using a tangential radiographic technique.

OBJECTIVE To assess whether there is a difference in the mechanical medial proximal tibial angle (mMPTA) measured on a tangential caudocranial (tCdCr) radiographic projection versus a straight caudocranial (sCdCr) projection before and after inducing a varus deformity in the proximal tibia. STUDY DESIGN In vitro study. SAMPLE POPULATION Cadaveric canine tibiae (n=4 pair). METHODS For each tibia, a mediolateral radiographic projection was performed and the tibial plateau angle was measured. sCdCr and tCdCr radiographic projections were obtained and the mMPTA measured. A varus deformity was created in the proximal aspect of the tibia and sCdCr and tCdCr projections were repeated and mMPTA measured. RESULTS mMPTA for tCdCr was statistically different from mMPTA for the sCdCr projection for the varus tibiae (P<.05). There was no significant difference in the mMPTA measured on the sCdCr projections before and after creation of a varus deformity (P>.05). There was a significant difference in mMPTA measured on the tCdCr projection before and after creation of a varus deformity (P<.05). CONCLUSION Varus deformity in the mMPTA was identified on tCdCr projections of the varus tibiae whereas it was not identified on sCdCr projections. CLINICAL RELEVANCE Tangential radiographic projections of the tibial plateau may be useful for evaluating varus deformities involving the articular surface of the tibia and should be performed during preoperative evaluation of angular limb deformities involving the proximal aspect of the tibia and for tibial plateau leveling osteotomy (TPLO) planning.
Electronic Excitations in Aggregates of Bacteriochlorophylls

Photosynthetic organisms have developed antenna systems to enlarge their cross section for capturing sunlight. These systems involve in some cases aggregates of bacteriochlorophylls (BChls). The structure of one such aggregate, a tightly coupled circular hexadecamer of BChls and a loosely coupled octamer of BChls, has recently been solved. In this paper we investigate the electronic excitations in these two aggregates as well as in monomeric BChl and BChl dimers by means of INDO/S-CI calculations. The results provide a detailed description of the properties of electronic states in the BChl aggregates (energies, dipole and transition dipole moments) that are relevant for the biological function of BChls, to absorb light and transfer energy on the subpicosecond time scale. The lower-energy excitations of the BChl hexadecamer are of exciton type, i.e., experiencing a strong coupling that leads to excitation delocalization over the entire aggregate. An effective Hamiltonian is provided which reproduces these .
Rapid identification of a point mutation of the Mycobacterium tuberculosis catalase-peroxidase (katG) gene associated with isoniazid resistance.

The complete catalase-peroxidase (katG) gene DNA sequence was determined for 15 strains of Mycobacterium tuberculosis with a wide range of susceptibility to isoniazid. Five of 9 strains with isoniazid MICs > or = 1.0 microgram/mL had one or more missense mutations and all 5 strains had a common G-->T transversion in codon 463, causing the replacement of arginine with leucine and the loss of an NciI or MspI restriction site. None of 6 strains with an isoniazid MIC < 1.0 microgram/mL had mutations affecting codon 463. Restriction analysis of 43 strains with isoniazid MICs > or = 1.0 microgram/mL showed that 19 (44.2%) had lost the NciI-MspI restriction site at the locus of codon 463 while only 1 of 32 strains with isoniazid MICs < or = 1.0 microgram/L had this restriction polymorphism. These results indicate that the mutation arginine-->leucine in codon 463 of the catalase-peroxidase gene occurs in a significant fraction (44.2%) of M. tuberculosis strains with isoniazid MICs > or = 1.0 microgram/mL.
Gene-selective modulation by a synthetic oxysterol ligand of the liver X receptor Published, JLR Papers in Press, August 1, 2004. DOI 10.1194/jlr.M400257-JLR200

Liver X receptors (LXRs) play key roles in the regulation of cholesterol homeostasis by limiting cholesterol accumulation in macrophages within arterial wall lesion sites by a mechanism that includes the upregulation of ATP binding cassette transporters. These atheroprotective properties distinguish LXRs as potential targets for pharmaceutical intervention in cardiovascular disease. Their associated activity for promoting lipogenesis and triglyceride accretion through the activation of sterol-response element binding protein 1c (SREBP-1c) expression, however, represents a potential proatherogenic liability. A newly characterized synthetic oxysterol, N,N-dimethyl-3β-hydroxycholenamide (DMHCA), represents a gene-selective LXR modulator that mediates potent transcriptional activation of ABCA1 gene expression while exhibiting minimal effects on SREBP-1c both in vitro and in vivo in mice. DMHCA has the potential to stimulate cholesterol transport through the upregulation of LXR target genes, including ABCA1, in liver, small intestine, and peritoneal macrophages. Compared with known nonsteroidal LXR agonists, however, DMHCA exhibits only limited activity for increasing hepatic SREBP-1c mRNA and does not alter circulating plasma triglycerides. Cell-based studies also indicate that DMHCA enhances cholesterol efflux in macrophages and suggest a mechanism whereby this selective modulator can potentially inhibit cholesterol accumulation. DMHCA and related gene-selective ligands of LXR may have application to the study and treatment of atherosclerosis.
SIMULTANEOUS ISOLATION OF PURIFIED MICROSOMAL and MYELIN FRACTIONS FROM RAT SPINAL CORD

Abstract— The fraction that sediments between 2 × 105g‐min and 6 × 106g‐min from dilute dispersions of rat brain in 0.32 m‐sucrose is a microsomal fraction with very little contamination by myelin. A crude microsomal fraction prepared in the same way from rat spinal cord contains more myelin than microsomes. Centrifugation of the crude microsomal fraction in 0.85 m‐sucrose gave a floating fraction, an infranatant fraction (purified microsomes) and a small pellet. The purified microsomes contained very little myelin as judged by electron microscopy and polyacrylamide gel electrophoresis. The lipid composition resembled that of spinal cord myelin except that the purified microsomes contained relatively less cholesterol and ethanolamine plasmalogens. The content of galactolipids was much greater in spinal cord microsomes than in brain microsomes. The spinal cord CDP‐ethanol‐amine:diglyceride ethanolaminephosphotransferase activity (EC 2.7.8.1) was concentrated in the purified microsomes.
A high susceptibility of Fanconi's anemia to chromosome breakage by DNA cross-linking agents.

Summary Peripheral blood lymphocytes of patients with Fanconi9s anemia (FA) were tested for their susceptibility to chromosome breakage by caffeine, chloramphenicol, actinomycin D, methylmethanesulfonate, nitrogen mustard, mitomycin C, decarbamoyl mitomycin C, N -methyl- N′ -nitro- N -nitrosoguanidine, 4-nitroquinoline 1-oxide, 8-methoxypsoralen, and 60 Co γ-ray and ultiviolet irradiations. A definitely abnormal response of the chromosomes of the FA cells was found when they were treated with nitrogen mustard and mitomycin C and after the irradiation with long-wavelength ultraviolet light in the presence of 8-methoxypsoralen. The specifically increased susceptibility to these compounds, which can introduce interstrand cross-links into DNA, is interpreted as an indication that the FA cells are defective in the repair mechanism to tolerate the cross-links produced in their DNA. The impairment of the capacity to tolerate the lesions produced in DNA may be implicated in the increased risk to develop malignant neoplasms in this hereditary disorder.
Critical Role for Alpha/Beta and Gamma Interferons in Persistence of Lymphocytic Choriomeningitis Virus by Clonal Exhaustion of Cytotoxic T Cells

ABSTRACT Under conditions of high antigenic load during infection with invasive lymphocytic choriomeningitis virus (LCMV) strains, virus can persist by selective clonal exhaustion of antigen-specific CD8+ T cells. In this work we studied the down-regulation of the virus-specific CD8+-T-cell response during a persistent infection of adult mice, with particular emphasis on the contribution of the interferon response in promoting host defense. Studies were conducted by infecting mice deficient in receptors for type I (alpha/beta interferon [IFN-α/β]), type II (IFN-γ), and both type I and II IFNs with LCMV isolates that vary in their capacity to induce T-cell exhaustion. The main conclusions of this study are as follows. (i) IFNs play a critical role in LCMV infection by reducing viral loads in the initial stages of infection and thus modifying both the extent of CD8+-T-cell exhaustion and the course of infection. The importance of IFNs in this context varies with the biological properties of the LCMV strain. (ii) An inverse correlation exists between antigen persistence and responsiveness of virus-specific CD8+ T cells. This results in distinct programs of activation or tolerance (functional unresponsiveness and/or physical elimination of antigen-specific cells) during acute and chronic virus infections, respectively. (iii) A successful immune response associated with definitive viral clearance requires an appropriate balance between cellular and humoral components of the immune system. We discuss the role of IFNs in influencing virus-specific T cells that determine the outcome of persistent infections.
Association of Actinobacillus pleuropneumoniae Capsular Polysaccharide with Virulence in Pigs

ABSTRACT The capsular polysaccharide (CP) of Actinobacillus pleuropneumoniae is required for virulence of the bacteria in swine. However, a molecular investigation of whether the type or quantity of CP affects A. pleuropneumoniae virulence has not been reported. To initiate this investigation, a DNA region downstream of conserved genes required for CP export in A. pleuropneumoniae serotype 1 was cloned and sequenced. Three open reading frames, designated cps1A, cps1B, and cps1C, were identified that had amino acid homology to bacterial carbohydrate biosynthesis genes. A kanamycin resistance cassette (Kanr) was inserted into a 750-bp deletion spanning cps1AB or into a 512-bp deletion in cps1B only, and the constructs were cloned in a suicide vector. The Kanr gene was then transferred into the chromosome of strain 4074 by homologous recombination to produce strain 4074Δcps1N and strain 4074Δcps1B, respectively. Strain 4074Δcps1N produced no detectable CP, but strain 4074Δcps1B made 15% of the serotype 1 CP made by the parent strain, 4074, as determined by enzyme-linked immunosorbent assay and precipitation of free CP. The cps1ABC genes of strain 4074 and the cps5ABC and cps5ABCDE genes of serotype 5a strain J45 were cloned into the shuttle vector pLS88 and electroporated into 4074Δcps1N to produce 4074Δcps1N(pABcps101), 4074Δcps1N(pJMLcps53), and 4074Δcps1N(pABcps55), respectively. Strain 4074Δcps1N(pABcps101) produced about 33% of the serotype 1 CP produced by strain 4074. Strains 4074Δcps1N(pJMLcps53) and 4074Δcps1N(pABcps55) produced serotype 5a CP in similar quantity or in fourfold excess, respectively, to that produced by strain 4074. With intratracheal challenge in pigs at similar dosages, the order of virulence of strains producing serotype 1 CP (assessed by mortality, lung consolidation, hemorrhage, and fibrinous pleuritis) was the following: strain 4074 > strain 4074Δcps1N(pABcps101) ≥ strain 4074Δcps1N > strain 4074Δcps1B. Strain 4074Δcps1N(pJMLcps53) was less virulent than strain 4074Δcps1N(pABcps55). However, both strains produced serotype 5a CP in similar or greater quantities than was observed for production of serotype 1 CP by the parent strain, 4074, but were less virulent than the parent strain. Therefore, the amount of serotype 1 or 5a CP produced by isogenic strains of A. pleuropneumoniae correlated with the virulence of the bacteria in pigs. However, virulence was also influenced by the type of CP produced or by its mechanism of expression.
Insulin‐like growth factor 1 is essential for normal dendritic growth

This study evaluated somatic and dendritic growth of neurons in the frontoparietal cortex of Igf1–/– brains. Pyramidal neuron density was increased by ∼25% (P = .005) and soma size reduced by ∼10% (P < .001). Golgi staining revealed that cortical layer II–III neurons exhibited a significant reduction in dendritic length and complexity in Igf1 null mice. Dendritic spine density and presumably synaptic contacts were reduced by 16% (P = .002). Similar findings were obtained for cortical layer V and piriform cortex pyramids. Supporting a reduction in synapses, synaptotagmin levels were reduced by 30% (P < .02) in the Igf1 null brain. Investigation of factors critically involved in dendritic growth and synaptogenesis showed an ∼50% reduction in cortical CDC42 protein expression (P < .001) and an ∼10% reduction in brain cholesterol levels (P < .01) in Igf1 null mice. Evidence is presented that Igf1 deletion causes disruptions in lipid and microtubule metabolism, leading to impaired neuronal somatic and dendritic growth. Published 2003 Wiley‐Liss, Inc.
Channel Norm-Based Power Control in Downlink Multi-User Distributed MIMO Systems

We consider distributed multiple-input multiple-output systems with remote antennas (RA) connected to the base station via high-capacity backhaul, which are operated under the per-antenna power constraint (PAPC). We propose a simple strategy to determie transmission power for each user, referred to as channel norm-based power control (NBPC) to obtain near-optimal performance in terms of the sum-rate maximization and the log-sum-rate maximization for fairness improvement, applicable to any number of RAs and users. In particular, a closed-form solution to maximize the sum-rate using the NBPC is presented. We also show that the proposed strategy used in conjunction with existing multi-user transmission schemes derived under the total power constraint can be efficiently applied to systems under the PAPC.
A Hybrid Approach for Three-Dimensional Building Reconstruction in Indianapolis from LiDAR Data

3D building models with prototypical roofs are more valuable in many applications than 2D building footprints. This research proposes a hybrid approach, combining the data- and model-driven approaches for generating LoD2-level building models by using medium resolution (0.91 m) LiDAR nDSM, the 2D building footprint and the high resolution orthophoto for the City of Indianapolis, USA. The main objective is to develop a GIS-based procedure for automatic reconstruction of complex building roof structures in a large area with high accuracy, but without requiring high-density point data clouds and computationally-intensive algorithms. A multi-stage strategy, which combined step-edge detection, roof model selection and ridge detection techniques, was adopted to extract key features and to obtain prior knowledge for 3D building reconstruction. The entire roof can be reconstructed successfully by assembling basic models after their shapes were reconstructed. This research finally created a 3D city model at the Level of Detail 2 (LoD2) according to the CityGML standard for the downtown area of Indianapolis (included 519 buildings). The reconstruction achieved 90.6% completeness and 96% correctness for seven tested buildings whose roofs were mixed by different shapes of structures. Moreover, 86.3% of completeness and 90.9% of correctness were achieved for 38 commercial buildings with complex roof structures in the downtown area, which indicated that the proposed method had the ability for large-area building reconstruction. The major contribution of this paper lies in designing an efficient method to reconstruct complex buildings, such as those with irregular footprints and roof structures with flat, shed and tiled sub-structures mixed together. It overcomes the limitation that building reconstruction using coarse resolution LiDAR nDSM cannot be based on precise horizontal ridge locations, by adopting a novel ridge detection method.
Ber‐EP4 enhances the differential diagnostic accuracy of cytokeratin 7 in pagetoid cutaneous neoplasms

Background: While cytokeratin 7 is a reliable marker for most cases of Paget’s disease, it is not 100% sensitive. Moreover, cases of cytokeratin 7‐positive pagetoid squamous cell carcinoma in situ are reported in the literature. The monoclonal antibody Ber‐EP4 is diagnostically highly reliable in the differentiation between basal cell carcinoma and cutaneous squamous cell carcinoma. Here we report its application in the differential diagnosis of cutaneous pagetoid neoplasms.
[Relation between single nucleotide polymorphism in estrogen-metabolizing genes COMT, CYP17 and breast cancer risk among Chinese women].

OBJECTIVE To test the hypothesis whether polymorphism in estrogen-metabolizing genes, COMT and CYP17, impacts on the risk of breast cancer among Chinese women. METHODS COMT (Val158Met) and CYP17 (T1931C) polymorphisms were detected by PCR-based restriction fragment length polymorphism analysis in 250 breast cancer patients and 250 frequency-matched normal controls. Odds ratios (ORs) and 95% confidence intervals (CIs) were estimated by unconditional logistic regression. RESULTS COMT Met/Met genotype was found in 10.4% of breast cancer patients, which was significantly higher (P = 0.03) than that in controls (5.2%). Women with Met/Met genotype showed 2-fold increased risk for breast cancer (adjusted OR 2.1, 95% CI 1.1 - 4.5) compared with those with Val/Val or Val/Met genotypes. Stratified analysis showed that the elevated risk of breast cancer, associating with the COMT Met/Met genotype, was evident only among premenopausal women (adjusted OR 4.1, 95% CI 1.2 - 17.3) but not among postmenopausal women (adjusted OR 1.3, 95% CI 0.5 - 3.5). There was no significant difference in the distribution of CYP17 genotypes between breast cancer patients and the control subjects (P = 0.83). CONCLUSION The allele encoding for low activity COMT, but not CYP17, may be a genetic risk factor for breast cancer among Chinese women.
Search and Coherence-Building in Intuition and Insight Problem Solving

Coherence-building is a key concept for a better understanding of the underlying mechanisms of intuition and insight problem solving. There are several accounts that address certain aspects of coherence-building. However, there is still no proper framework defining the general principles of coherence-building. We propose a four-stage model of coherence-building. The first stage starts with spreading activation restricted by constraints. This dynamic is a well-defined rule based process. The second stage is characterized by detecting a coherent state. We adopted a fluency account assuming that the ease of information processing indicates the realization of a coherent state. The third stage is designated to evaluate the result of the coherence-building process and assess whether the given problem is solved or not. If the coherent state does not fit the requirements of the task, the process re-enters at stage 1. These three stages characterize intuition. For insight problem solving a fourth stage is necessary, which restructures the given representation after repeated failure, so that a new search space results. The new search space enables new coherent states. We provide a review of the most important findings, outline our model, present a large number of examples, deduce potential new paradigms and measures that might help to decipher the underlying cognitive processes.
Combining acoustic name spotting and continuous context models to improve spoken person name recognition in speech

Retrieving pronounced person names in spoken documents is a critical problematic in the context of audiovisual content indexing. In this paper, we present a cascading strategy for two methods dedicated to spoken name recognition in speech. The first method is an acoustic name spotting in phoneme confusion networks. It is based on a phonetic edition distance criterion based on phoneme probabilities held in confusion networks. The second method is a continuous context modelling approach applied on the 1-best transcription output. It relies on a probabilistic modelling of name-to-context dependencies. We assume that the combination of these methods, based on different types of information, may improve spoken name recognition performance. This assumption is studied through experiments done on a set of audiovisual documents from the development set of the REPERE challenge. Results report that combining acoustic and linguistic methods produces an absolute gain of 3% in terms of F-measure compared to the best system taken alone.
pH-specific sequestration of phosphoglucose isomerase/autocrine motility factor by fibronectin and heparan sulphate

Phosphoglucose isomerase (PGI) is a glycolytic enzyme that moonlights as a cytokine under the aliases autocrine motility factor (AMF), neuroleukin and maturation factor. The cytokine function of PGI/AMF targets multiple cell types however mechanisms that regulate and sequester this ubiquitous, circulating cytokine remain largely unidentified. PGI/AMF is shown here to exhibit fibronectin (FN)-dependent cell surface association at both neutral and acid pH. Direct PGI/AMF binding to FN and fluorescence resonance energy transfer (FRET) between PGI/AMF and FN were detected only at pH 5. At neutral pH, the interaction of PGI/AMF with FN is receptor-mediated requiring prior clathrin-dependent endocytosis. PGI/AMF and FN do not co-internalize and PGI/AMF undergoes a second round of endocytosis upon recycling to the plasma membrane indicating that recycling PGI/AMF receptor complexes associate with FN fibrils. Heparan sulphate does not affect cell association of PGI/AMF at neutral pH but enhances the FN-independent cell surface association of PGI/AMF at acid pH identifying two distinct mechanisms for PGI/AMF sequestration under acidic conditions. However, only PGI/AMF sequestration by FN at acid pH was able to stimulate cell motility upon pH neutralization identifying FN as a pH-dependent cytokine trap for PGI/AMF. The multiple ways of cellular association of PGI/AMF may represent acquired mechanisms to regulate and harness the cytokine function of PGI/AMF.