Miracle-dz/UniFAR-FTUs huggingface dataset:
POLYGENIC RESISTANCE OF IMPROVED RED PEPPER LINES TO PHYTOPHTHORA CAPSICI

Belonging to the Oomycete genus, Phytophthora capsici is responsible of many devastating disease and the most destructive agent of pepper in the World. The most cost-effective method for preventing Phytophthora blight is to use resistant cultivars. In this study, the polygenic resistance of improved pepper lines to Phytophthora Blight were screened by molecular markers placed on three chromosomes in pepper. Sena variety registered as suitable for spice pepper production was used as susceptible female donor and CM 334 and Perennial genotypes were used as male resistance sources. Thirty two genotypes were screened by ASC 035 marker placed on chromosomes P10, ASC 037 on P5 and ASC 031 on P2. Twelve of these improved red pepper lines from different resistance sources were exhibited polygenic resistance according to electrophoretic signals to all of three markers placed on P2, P5 and P10. In order to determine codominance of the resistance genes PCR products of ASC 031 and ASC 037 were restricted by HaeIII and EcoRI respectively. Ten improved lines exhibited codominance related with resistance to Phytophthora Blight concerning ASC 031 and only one line was showed codominance for ASC 037. Three different lines had one resistance gene on P5 and on P10 independently. Only T12 line holds two resistance genes both P2 and P10. DD and 63 lines were most promising genotypes related with their resistance to pathogen. Molecular assisted selection was found useful for improving Phytophthora resistant red pepper lines.
Adeno-associated virus type 2-mediated transfer of ecotropic retrovirus receptor cDNA allows ecotropic retroviral transduction of established and primary human cells

The cellular receptors that mediate binding and internalization of retroviruses have recently been identified. The concentration and accessibility of these receptors are critical determinants in accomplishing successful gene transfer with retrovirus-based vectors. Murine retroviruses containing ecotropic glycoproteins do not infect human cells since human cells do not express the receptor that binds the ecotropic glycoproteins. To enable human cells to become permissive for ecotropic retrovirus-mediated gene transfer, we have developed a recombinant adeno-associated virus type 2 (AAV) vector containing ecotropic retroviral receptor (ecoR) cDNA under the control of the Rous sarcoma virus (RSV) long terminal repeat (LTR) promoter (vRSVp-ecoR). Established human cell lines, such as HeLa and KB, known to be nonpermissive for murine ecotropic retroviruses, became permissive for infection by a retroviral vector containing a bacterial gene for resistance to neomycin (RV-Neo(r)), with a transduction efficiency of up to 47%, following transduction with vRSVp-ecoR, as determined by the development of colonies that were resistant to the drug G418, a neomycin analog. No G418-resistant colonies were present in cultures infected with either vRSVp-ecoR or RV-Neo(r) alone. Southern and Northern blot analyses revealed stable integration and long-term expression, respectively, of the transduced murine ecoR gene in clonal isolates of HeLa and KB cells. Similarly, ecotropic retrovirus-mediated Neo(r) transduction of primary human CD34+ hematopoietic progenitor cells from normal bone marrow was also documented, but only following infection with vRSVp-ecoR. The retroviral transduction efficiency was approximately 7% without prestimulation and approximately 14% with prestimulation of CD34+ cells with cytokines, as determined by hematopoietic clonogenic assays. No G418-resistant progenitor cell colonies were present in cultures infected with either vRSVp-ecoR or RV-Neo(r) alone. These results suggest that sequential transduction of primary human cells with two different viral vectors may overcome limitations encountered with a single vector. Thus, the combined use of AAV- and retrovirus-based vectors may have important clinical implications for ex vivo and in vivo human gene therapy.
Protection of Rhesus Monkeys against Infection with Minimally Pathogenic Simian-Human Immunodeficiency Virus: Correlations with Neutralizing Antibodies and Cytotoxic T Cells

ABSTRACT We studied the capacity of active immunization of rhesus monkeys with HIV-1 envelope protein (Env) to induce primary virus cross-reactive neutralizing antibodies to prevent infection following intravenous challenge with simian-human immunodeficiency virus (SHIV). Monkeys were immunized with the human immunodeficiency type 1 (HIV-1) strain R2 Env. Initially, the Env was expressed in vivo by an alphavirus replicon particle system, and then it was administered as soluble oligomeric gp140. Concurrently, groups of monkeys received expression vectors that encoded either simian immunodeficiency virus (SIV) gag/pol genes or no SIV genes in vivo to test the additional protective benefit of concurrent induction of virus-specific cell-mediated immune (CMI) responses. Groups of control monkeys received either the gag/pol regimen or sham immunizations. The antibodies induced by the Env immunization regimen neutralized diverse primary HIV-1 strains. Similarly, potent CMI responses were induced by the gag/pol regimen, as measured by gamma interferon enzyme-linked immunospot assays. Differences in the responses among groups of monkeys strongly suggested that there was interference between the Env and gag/pol immunization regimens. Complete protection of some of the monkeys against infection after intravenous challenge with the partially pathogenic SHIVDH12R (Clone 7) was associated independently with both neutralizing antibody and CMI responses. Protection was associated with SHIVDH12 (Clone 7) serum neutralizing antibody titers of ≥1:80 or with cellular immune responses corresponding to >2,000 spot forming cells per 106 peripheral blood mononuclear cells. Immunization was also associated with a reduction in the magnitude and duration of virus load. Induction of cross-reactive, primary HIV-1-neutralizing antibodies is feasible and, when potent, may result in complete protection against infection with a heterologous challenge virus strain.
The photoactive site modulates current rectification and channel closing in the natural anion channelrhodopsin GtACR1

The crystal structure of GtACR1 from Guillardia theta revealed an intramolecular tunnel predicted to expand to form the anion-conducting channel upon photoactivation (Li et al. 2019). The location of the retinylidene photoactive site within the tunnel raised the question of whether, in addition to triggering channel opening by photoisomerization, the site also participates in later channel processes. Here we demonstrate the involvement of the photoactive site in chloride conductance and channel closing. Electrostatic perturbation of the photoactive retinylidene Schiff base region by glutamate substitutions alters the rectification of the photocurrent as well as channel closing kinetics. Substitutions on opposite sides of the photoactive site causes opposite changes, with channel closing kinetically correlated with Schiff base deprotonation, and the extent of these effects closely correlate with distance of the introduced glutamyl residue from the photoactive site.
Improving the Performance of LVCSR Using Ensemble of Acoustic Models

Recent advances in Machine Learning have brought to attention new theories of learning as well as new approaches. Among these, the Ensemble method has received wide attention and has been shown to be a promising method for classification problems. Simply speaking, the ensemble method is a learning algorithm that constructs a set of “weak” classifiers and then combines their predictions to produce a more accurate classification. The underlying idea of the ensemble method is that the combination of diversified classifiers that have uncorrelated, and ideally complementary, error patterns can offer improved performance and a robust generalization capability. Given its successes for many classification problems, we began investigating the problem of adapting ensemble techniques to continuous speech recognition. Continuous Speech Recognition has been acknowledged as one of the most challenging tasks in classification. The performance of an ASR system is negatively impacted by a number of issues, such as corruption of noise, variability of speaker and speaking mode, change of environment conditions, transmission of channel, inaccuracy of model assumption, complexity of language, etc. The primary goal of our research is to discover methods suitable for ensemble construction and combination that meet these special requirements of continuous speech recognition. We propose several novel ensemble-based acoustic model training and combination schemes, and test their effectiveness using real-world speech corpora. Preliminary results are described in this proposal, in particular • Utterance-level Boosting training algorithm for large scale acoustic modeling • Frame-level Boosting training algorithm using a Word Error Rate reduction criterion • N-Best list re-ranking and Rover combination to generate a better hypothesis Encouraging experimental results convince us that the ensemble technique is a promising method and that it has the potential to substantially improve the performance of a LVCSR system. However research on ensemble methods for speech recognition is still in its early stage and unsolved questions on ensemble generation and hypothesis combination remain to be addressed. This proposal sets out several key research topics that, if successfully addressed will have the potential to significantly increase the accuracy of ensemble-based speech recognition systems. These include the following: • Training criteria targeted at reducing Word Error Rate rather than Sentence Error Rate. • Integrating data manipulation and feature manipulation methods for continuous speech recognition. • Combination methods working on different objects, different levels and different decoding stages. • Ensemble-based semi-supervised acoustic model training algorithm using labeled and unlabeled data.
A Bronze Age Round Barrow Cemetery, Pit Alignments, Iron Age Burials, Iron Age Copper Working, and Later Activity at Four Crosses, Llandysilio, Powys

Excavation undertaken at the Upper Severn valley round barrow cemetery at Four Crosses, Llandysilio, Powys, between 2004 and 2006 has increased the known barrows and ring ditches to some twenty-seven monuments within this complex, and revealed additional burials. Based on limited dating evidence, and the data from earlier excavations, the majority of the barrows are thought to be constructed in the Bronze Age. The barrows are considered part of a larger linear cemetery. The landscape setting and wider significance of this linear barrow cemetery are explored within this report. Dating suggests two barrows were later, Iron Age additions. The excavation also investigated Iron Age and undated pit alignments, Middle Iron Age copper working and a small Romano-British inhumation cemetery and field systems. Much of this evidence reflects the continuing importance of the site for ritual and funerary activity.
Extraction of building's geometric axis line from LiDAR data for disaster management

Fast and reliable building damage analysis is crucial for survivors rescue and disaster management when a destructive natural disaster occurs which helps to limit life losses. For this purpose, a method was developed in this paper to extract building's geometric axis line from aerial LiDAR data which helps to do further building damage analysis like to identify inclined buildings. To extract building's geometric axis line, several steps were carried out such as segmentation of buildings, extraction of roof facets, fitting of mean roof plane and getting main roof. The aerial LiDAR data was captured over the area of Port-au-Prince, Haiti which contains numerous of inclined buildings. The results demonstrate the feasibility and effectiveness of the proposed approach to identify inclined building for damage management.
Novel cAMP signalling paradigms: therapeutic implications for airway disease

Since its discovery over 50 years ago, cAMP has been the archetypal second messenger introducing students to the concept of cell signalling at the simplest level. As explored in this review, however, there are many more facets to cAMP signalling than the path from Gs‐coupled receptor to adenylyl cyclase (AC) to cAMP to PKA to biological effect. After a brief description of this canonical cAMP signalling pathway, a snapshot is provided of the novel paradigms of cAMP signalling. As in the airway the cAMP pathway relays the major bronchorelaxant signal and as such is the target for frontline therapy for asthma and COPD, particular emphasis is given to airway disease and therapy. Areas discussed include biased agonism, continued signalling following internalization, modulation of cAMP by AC, control of cAMP degradation, cAMP and calcium crosstalk, Epac‐mediated signalling and finally the implications of altered genotypes will be considered.
Associations between Polymorphisms in DNA Repair Genes and Glioblastoma

A pooled analysis was conducted to examine the association between select variants in DNA repair genes and glioblastoma multiforme, the most common and deadliest form of adult brain tumors. Genetic data for ∼1,000 glioblastoma multiforme cases and 2,000 controls were combined from four centers in the United States that have conducted case-control studies on adult glioblastoma multiforme, including the National Cancer Institute, the National Institute for Occupational Safety and Health, the University of Texas M. D. Anderson Cancer Center, and the University of California at San Francisco. Twelve DNA repair single-nucleotide polymorphisms were selected for investigation in the pilot collaborative project. The C allele of the PARP1 rs1136410 variant was associated with a 20% reduction in risk for glioblastoma multiforme (odds ratioCT or CC, 0.80; 95% confidence interval, 0.67-0.95). A 44% increase in risk for glioblastoma multiforme was found for individuals homozygous for the G allele of the PRKDC rs7003908 variant (odds ratioGG, 1.44; 95% confidence interval, 1.13-1.84); there was a statistically significant trend (P = 0.009) with increasing number of G alleles. A significant, protective effect was found when three single-nucleotide polymorphisms (ERCC2 rs13181, ERCC1 rs3212986, and GLTSCR1 rs1035938) located near each other on chromosome 19 were modeled as a haplotype. The most common haplotype (AGC) was associated with a 23% reduction in risk (P = 0.03) compared with all other haplotypes combined. Few studies have reported on the associations between variants in DNA repair genes and brain tumors, and few specifically have examined their impact on glioblastoma multiforme. Our results suggest that common variation in DNA repair genes may be associated with risk for glioblastoma multiforme. (Cancer Epidemiol Biomarkers Prev 2009;18(4):1118–26)
Prevalence of the mutational pattern E44D/A and/or V118I in the reverse transcriptase (RT) gene of HIV‐1 in relation to treatment with nucleoside analogue RT inhibitors

It has been reported that a new pattern of mutations, E44D/A and/or V118I, in the reverse transcriptase (RT) gene of HIV‐1 confers a moderate level of resistance to lamivudine in the absence of the M184V mutation. The prevalence of this mutational pattern was studied in HIV‐1 isolates obtained from 280 patients. These mutations were not identified in the RT sequences from 23 antiretroviral‐naive patients but were detected in 82 (31.9%) of the 257 RT sequences obtained from nucleoside reverse transcriptase inhibitors (NRTI)‐experienced patients. Mutation at codon 44 was identified in 41 patients (7 mutations E44A and 34 mutations E44D), mutation V118I was identified in 73 patients and a combination of mutations at codons 44 and 118 was found in 32 patients. Multivariate analysis showed an association between the E44D/A and/or V118I mutational pattern and the RT mutations D67N, T69D, L210W, and T215Y/F. No relationship was observed between this mutational pattern and the lamivudine‐specific resistance mutation M184V. The prevalence of these mutations increased significantly with the number of drug regimens experienced and a prevalence of 42.4% was observed in patients who had received ≥ 4 antiretroviral regimens. A relationship was found between the E44D/A and/or V118I mutational pattern and experience with didanosine or stavudine but not with lamivudine. The results suggest that the development of the E44D/A and/or V118I mutational pattern is frequent in patients treated with NRTIs. Thymidine analogues and didanosine, but not lamivudine, could promote the development of these mutations. J. Med. Virol. 66:299‐303, 2002. © 2002 Wiley‐Liss, Inc.
Glucose Reduction Prevents Replicative Senescence and Increases Mitochondrial Respiration in Human Mesenchymal Stem Cells

The unique self-renewal and multilineage differentiation potential of mesenchymal stem cells (MSCs) make them a promising candidate for cell therapy applications. However, during in vitro expansion of MSCs, replicative senescence may occur and will compromise the quality of the expanded cells. Because calorie restriction has been shown to effectively extend the life span of various organisms, the purpose of this study is to investigate the effect of glucose reduction on MSCs and the coordinated changes in energy utilization. It was found that the frequency of cycling cells was significantly increased, while senescence markers such as β-galactosidase activities and p16INK4a expression level were markedly reduced in MSCs under low-glucose culture condition. Quantitative real-time PCR analysis demonstrated the preserved trilineage differentiation potentials of MSCs after low-glucose treatment. Interestingly, the ability of osteogenic lineage commitment was improved, while the ability of adipogenic lineage commitment was delayed in MSCs after glucose reduction. In addition, we observed decreased lactate production, increased electron transport chain complexes expression, and increased oxygen consumption in MSCs after glucose reduction treatment. Increased antioxidant defensive responses were evidenced by increased antioxidant enzymes expression and decreased superoxide production after glucose reduction. Taken together, our findings suggest that MSCs utilize energy more efficiently under restricted glucose treatment and exhibit greater self-renewal and antisenescence abilities, while their differentiation potentials remain unaffected.
The bacterial DNA-binding protein H-NS represses ribosomal RNA transcription by trapping RNA polymerase in the initiation complex.

The interaction of the bacterial regulatory protein H-NS with RNA polymerase and the ribosomal RNA P1 promoter was analyzed to better understand the mechanism of H-NS-dependent transcriptional repression. We could show that initial binding of RNA polymerase to the promoter was not inhibited by the simultaneous interaction of H-NS, although H-NS binding sites extend into the core promoter region. Binding of sigma(70)-saturated RNA polymerase and H-NS to the promoter DNA occurs cooperatively and results in a stable complex of slower gel electrophoretic mobility as compared to complexes formed with the single proteins. The presence of the upstream curved H-NS binding site contributes strongly to the cooperative RNA polymerase-promoter interaction. By KMnO(4) modification of single-stranded template nucleotides we could show that open complex formation at the rrnB P1 promoter was not inhibited by H-NS binding. An increased KMnO(4) reactivity of several positions within the open complex rather supports the view that open complex formation is stimulated in presence of H-NS. Moreover, subtle changes in the modification pattern indicate that the open complex formed in the presence of H-NS are structurally distinct from the H-NS-free complex. In vitro transcriptional analysis of the abortive and productive yields revealed that the formation of transcription products longer than three nucleotides is dramatically reduced in the presence of H-NS, while the amount of shorter abortive products remained unaffected. Together the results demonstrate that H-NS inhibits transcription at the rrnB P1 promoter not by interfering with initial RNA polymerase binding but by blocking chain elongation steps subsequent to the first (two) phosphodiester bond formations. The mechanism of H-NS dependent repression at rRNA promoters can thus be explained as a trap which inhibits substrate NTP incorporation beyond template position +3 into the initial transcribing complex.
Phase change in amylose-water mixtures as seen by Fourier transform infrared.

The phase content of amylose-water mixtures (0.7/0.3 w/w) has been analyzed by transmission Fourier transform infrared (FTIR) spectroscopy in the 1175-950 cm(-1) region. Spectra are obtained under three different conditions: (a) as a function of temperature (T) from 25 to 97 degrees C; (b) at room temperature (RT), after slow cycles of T; and (c) at RT after quenching. T(max), the maximum temperature in the cycle, ranges from 50 to 120 degrees C. The quality of the seven-band spectra allows for an unambiguous determination of each band area. Unexpectedly, slow cooling after different T(max) brings about wide changes in the spectra while quenching does not. Two jumps in the absorbance are found: one at 70 degrees C and the other above 105 degrees C. Previous work on slow calorimetry of amylose-water mixtures suggests that these temperatures correspond to the beginning and the end of the same physical phenomena that takes place slowly between these two temperatures-namely the dissolution of the strained network phase. The spectra have two distinct regions, the low wavenumber region (1078-950 cm(-1)) and the high wavenumber region (1175-1078 cm(-1)). A distinct gain in the integrated absorbance of the 1175-1078 cm(-1) region at the expanse of that of the 1078-950 cm(-1) region when T(max) increases is interpreted as a change from strained to unstrained environments. A nonequilibrium state between the chains is a strained environment. In light of the (13)C NMR evaluation of the change of molecular order with T, the observed changes of the ir spectra could correspond to a transformation of a network of double helices into freer chains, possibly single helices. The present in-depth analysis of equilibrium or near equilibrium states by FTIR can serve to understand, through in situ spectra, molecular mechanisms during the gelation/crystallization of amylose and other gel-forming polymers.
Management module based on SNMP for a warning message receiver considering DTT and FM

As a part of an Early Warning System, it has been developed a receiver of warning message, which has mainly DTT ISDB-T, FM RDS and Sound power submodules. This receiver is able to process warming messages over DTT and radio FM, with the purpose of activating an electronic siren and alerting to a neighboring population. In this context, this paper proposes a management module based on SNMP for the warning message receiver. For this, we have developed a MIB module and we have worked with AgentX protocol for the extension of SNMP Agent.