58 research outputs found

    Gas-Phase Protein Structure Characterization with Ion Mobility Mass Spectrometry and Molecular Dynamics Simulations

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    Over the last few decades, the widespread application of soft ionization techniques such as electrospray ionization (ESI) coupled with mass spectrometry (MS) facilitated the characterization of large biomolecules in the gas phase. Under suitable conditions and during the short timescale of the desolvation process associated with ESI (10-12-102 s), the solvent-free protein ions preserve significant portions of their native solution-phase structure and are presumed to be kinetically protected from thermodynamic destabilization such as unfolding-refolding processes occurring in the gas phase that could yield an inside-out structure.;The combination of ESI with ion mobility spectrometry- mass spectrometry (IMS-MS) provides information regarding higher-order structure of proteins and their complexes. IMS-MS has the ability to resolve and probe conformers of protein ions of a particular charge state based on their mobility through an inert buffer gas in drift tube under the influence of a constant electric field. An ion\u27s mobility is dependent upon its charge and shape and can be used to determine the orientationally-averaged collision cross section (CCS) of the ion with the buffer gas. Comparison of experimentally measured CCS values with theoretical CCS numbers obtained from a series of computer-assisted molecular dynamics simulations (MD) which explore the conformational space of protein ions provides insight into candidate structures for each conformer.;Although, CCS values provide a rough estimate of the overall shape of different molecules, IMS-MS alone cannot distinguish three dimensional structures of a series of conformers that represent the same mobility and thus would arrive at the same time at the exit region of the drift tube. The combination of IMS-MS with hydrogen-deuterium exchange (HDX) experiments as a gas-phase chemical probe of structure provides the opportunity to distinguish among these conformer types.;In this work, the gas-phase ion conformers of a model peptide have been studied through CCS measurements, HDX behavior analysis and extensive (MD) simulations.;Initially, an advanced protocol is introduced in order to achieve an impartial sampling of phase space targeting both higher-energy and more thermodynamically-stable structures. The gas-phase transport properties of the ion conformers - including their dynamics at experimental temperatures- have been monitored, and, combined with an optimized clustering and data mining method, accurate CCS determination has been accomplished. These data provided the first criterion to filter through a substantial pool of conformations in order to obtain a series of candidate structures (CCS matched) with significant structural variation.;A hydrogen accessibility scoring (HAS)-number of effective collisions (NEC) model is applied to the candidate structures obtained from MD simulations. The HAS-NEC model produced hypothetical, per-residue deuterium uptake values. This information then provided the overall structural contribution from each in-silico structure leading to the best match to experimental results. The comparison of predicted and experimentally observed isotopic envelopes of various mass spectral fragment ions supported the accuracy of the model. With these results, the hypothetical HDX data were employed as a second dimension to narrow the sampled phase space and, together with the accurate CCS values, 13 nominal conformers with specific population contributions to the gas-phase ions were selected.;In the final installment of this work, extensive simulations of the ESI process were performed to monitor the behavior of the peptide ion, charge carriers and the droplets involved in the ionization process. The results provided a series of structures that match the nominal conformers obtained through CCS calculations and the HAS-NEC model. This method validation confirmed the accuracy of the HAS-NEC model in successfully predicting the representative gas-phase structures on a computationally-affordable timescale

    Multi-Label Feature Selection Using Adaptive and Transformed Relevance

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    Multi-label learning has emerged as a crucial paradigm in data analysis, addressing scenarios where instances are associated with multiple class labels simultaneously. With the growing prevalence of multi-label data across diverse applications, such as text and image classification, the significance of multi-label feature selection has become increasingly evident. This paper presents a novel information-theoretical filter-based multi-label feature selection, called ATR, with a new heuristic function. Incorporating a combinations of algorithm adaptation and problem transformation approaches, ATR ranks features considering individual labels as well as abstract label space discriminative powers. Our experimental studies encompass twelve benchmarks spanning various domains, demonstrating the superiority of our approach over ten state-of-the-art information-theoretical filter-based multi-label feature selection methods across six evaluation metrics. Furthermore, our experiments affirm the scalability of ATR for benchmarks characterized by extensive feature and label spaces. The codes are available at https://github.com/Sadegh28/ATRComment: 34 page

    Spatial Planning of Rural tourism with MAPPAC technique. Case study Khur and Biabanak County, (Iran)

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    Reviewing the concepts of space and tourism industry, tourism is in an old, deep, unbreakable bound with spatial and physical dimensions. In this way, the lack of systematic and scientific ranking process in spatial locating of rural tourism spots and also improper distribution of infrastructures are the critical deficiencies in this field. The research intends to introduce the hidden potentials and unique capabilities of Khur and Biabanak County, Iran. And prioritize their tourism spots. So tourism planners would be able to recognize proper space distribution. First, the weights of each criterion were calculated by a pairwise comparison questionnaire of AHP method, and MAPPAC technique was used for ranking. AHP was done in Expert Choice software and MAPPAC in MS Excel. Results showed that villages such as Bayaze, Jandagh, Mehrejan, Garmeh, and Iraj which are also older have a higher rank.Reviewing the concepts of space and tourism industry, tourism is in an old, deep, unbreakable bound with spatial and physical dimensions. In this way, the lack of systematic and scientific ranking process in spatial locating of rural tourism spots and also improper distribution of infrastructures are the critical deficiencies in this field. The research intends to introduce the hidden potentials and unique capabilities of Khur and Biabanak County, Iran. And prioritize their tourism spots. So tourism planners would be able to recognize proper space distribution. First, the weights of each criterion were calculated by a pairwise comparison questionnaire of AHP method, and MAPPAC technique was used for ranking. AHP was done in Expert Choice software and MAPPAC in MS Excel. Results showed that villages such as Bayaze, Jandagh, Mehrejan, Garmeh, and Iraj which are also older have a higher rank

    A social work study to investigate the relationships between women’s personal characteristics and employment status

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    Women play important role on building a sustainable family oriented society; they could also contribute to society by contributing to labor market. However, women’s personal characteristics such as educational background, years of experience, etc. could impact their future occupations. In this paper, we study the impact of various factors on women’s job status. The measurement tools for social factors of employment in this research is a questionnaire consists of 32 questions. The study measures the reflection of repliers to different social factors including social position, popularity, socialize, social manners, self-reliance, speech abilities, responsibility, etc. Data were gathered from a sample of 300 people using random sampling and analyzed using descriptive mono factor statistics, Spearman correlation, Kramer correlation coefficient, Chi-square, regression and path analysis. The validity of questionnaire is tested by using Cronbach alpha (%75). The results indicate that there are some meaningful relationships between woman’s educational level, age, residency status, socialization capability, urbanity, skill & ability and their employment. The study, however, does not find any relationship between marital status and number of children and outcome of woman’s employment

    Gonorrhea and syphilis co-infection and related risk factors in HIV patients from Shiraz, South of Iran

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    Background: Neisseria gonorrhea and Treponema pallidum as an obligate human pathogen are two common causes of sexually transmitted diseases (STDs). The present study aimed to determine the prevalence of N. gonorrhoeae and T. pallidum among human immunodeficiency virus (HIV) patients in the southwest Iran. Methods: This retrospective study was performed from 2004 to 2013, on HIV patients who were tested for detection of gonorrhea and syphilis infection at Shiraz HIV/AIDS Research Center. ELISA technique was used for preliminary detection of HIV and confirmed by a Western Blotting test. Gonorrhea was routinely diagnosed using direct Gram-staining and culturing on selective agar. Syphilis was routinely diagnosed by RPR test. Results: Of the 806 HIV patients, 39 (2.6%) cases had co-infection with gonorrhea. Compared with mono-HIV infected patients, gonorrhea was significantly more likely among the males (69.4% vs. 92.3%, P=0.002). History of addiction and prison seems to be a significant risk factor for gonorrhea infection (P<0.05). Also, the mean of CD4+lymphocyte was higher among gonorrhea infected patients (368 +/- 238 vs. 415 +/- 328). Logistic regression analysis showed that sexual contact increased risk of gonococcal infection about 4 fold (OR: 4, CI: 1.7-9.39, P=0.001). None of the HIV patients had syphilis co-infection. Conclusions: As a preliminary survey, our findings provided unique information on the prevalence of gonorrhea and syphilis co-infections among HIV patients. Moreover, we introduced the main risk factors associated with gonorrhea co-infection in HIV patients in our region including gender, history of addiction and prison, CD4+lymphocyte count, and transmission routes for effective management of STDs

    Gonor¬rhea and syphilis co-infection and related risk factors in HIV patients from Shiraz, South of Iran

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    Background: Neisseria gonorrhea and Treponema pallidum as an obligate human pathogen are two common causes of sexually transmitted diseases (STDs). The present study aimed to determine the prevalence of N. gonorrhoeae and T. pallidum among human immunodeficiency virus (HIV) patients in the southwest Iran. Methods: This retrospective study was performed from 2004 to 2013, on HIV patients who were tested for detection of gonorrhea and syphilis infection at Shiraz HIV/AIDS Research Center. ELISA technique was used for preliminary detection of HIV and confirmed by a Western Blotting test. Gonorrhea was routinely diagnosed using direct Gram-staining and culturing on selective agar. Syphilis was routinely diagnosed by RPR test. Results: Of the 806 HIV patients, 39 (2.6%) cases had co-infection with gonor¬rhea. Compared with mono-HIV infected patients, gonor¬rhea was significantly more likely among the males (69.4% vs. 92.3%, P=0.002). History of addiction and prison seems to be a significant risk factor for gonor¬rhea infection (P<0.05). Also, the mean of CD4+lymphocyte was higher among gonor¬rhea infected patients (368±238 vs. 415±328). Logistic regression analysis showed that sexual contact increased risk of gonococcal infection about 4 fold (OR: 4, CI: 1.7-9.39, P=0.001). None of the HIV patients had syphilis co-infection. Conclusions: As a preliminary survey, our findings provided unique information on the prevalence of gonorrhea and syphilis co-infections among HIV patients. Moreover, we introduced the main risk factors associated with gonorrhea co-infection in HIV patients in our region including gender, history of addiction and prison, CD4+lymphocyte count, and transmission routes for effective management of STDs

    IN-VITRO INVESTIGATION OF NUCLEOSOME DISPLACING FACTORS IN AFFECTING NUCLEOSOME ASSEMBLY AND REPOSITIONING

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    By wrapping the DNA around the histone core, nucleosomes intrinsically limit the availability of underlying DNA to variety of protein factors involved in vital cellular processes including transcription initiation, elongation, and termination. Reliable gene expression requires regulated access to DNA for RNA polymerase and transcription factors (TFs) to effectively engage with their binding sites embedded within the nucleosomes. Eukaryotes have evolved pathways to promote these interactions by altering the position of the histone core along the genomic DNA. In transcriptionally active genes, nucleosome positions in promoters are regulated by nucleosome displacing factors (NDFs) and chromatin remodeling enzymes. Depletion of NDFs or specific remodelers shrinks or abolishes the nucleosome depleted regions (NDRs), which can suppress gene activation and result in cryptic transcription. Despite their vital cellular functions, how the action of chromatin remodelers may be directly affected by site-specific binding factors like NDFs is poorly understood. Advanced in-vitro studies in characterizing the remodeling activity at a molecular level have provided significant insight into regulated histone core repositioning along DNA. Such studies in large rely on determining the precise histone-DNA contacts during chromatin remodeling events. Here, the results obtained from similar in-vitro studies show that NDFs bias the action of chromatin remodeling enzymes to increase the length of the free DNA in the vicinity of their binding sites. Although other factors are likely involved, these observations suggest that NDFs directly affect NDR architecture through chromatin remodelers. Although a comparable TF showed similar behavior, the stronger effects of NDFs are consistent with higher affinity for binding sites within the nucleosomal DNA. Thus, NDFs with high cellular concentrations appear to have a kinetic advantage in the context of the nucleosome. For hexasomes, the TF was as potent as NDFs in redirecting positioning of the histone core by the remodeler, suggesting that creation of subnucleosome assemblies may tune the sensitivity of chromatin remodeling to non-NDF proteins. Additionally, chaperone-mediated nucleosome assembly experiments here revealed a kinetic competition between NDFs and histone core proteins for DNA in vitro. Together, these observations provide an explanation for how NDFs may preferentially nucleate and maintain NDRs

    Lokal olmayan parametrenin uzaysal değişiminini göz önönde bulundurarak fonksıyonel derecelendirilmiş dıkdörtgen nano plakların serbest titreşim analizleri.

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    This study presents a new nonlocal elasticity based analysis method for free vibrations of functionally graded rectangular nano-plates. The method allows taking into account spatial variation of the nonlocal parameter. Governing partial differential equations and associated boundary conditions are derived by employing the variational approach and applying Hamilton’s principle. All required material properties are assumed to be functions of thickness coordinate in the derivations. Displacement field is expressed in a unified way to be able to produce numerical results pertaining to three different plate theories, namely Kirchhoff, Mindlin, and third-order shear deformation theories. The equations are solved numerically by means of the generalized differential quadrature method. Proposed procedures are verified through comparisons made to the results available in the literature. Further numerical results are generated by considering functionally graded simply-supported and cantilever nano-plates undergoing free vibrations. These findings demonstrate influences of factors such as dimensionless plate length, plate theory, nonlocal parameter ratio, and power-law index upon natural vibration frequencies.  M.S. - Master of Scienc
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