Miracle-dz/UniFAR-FTUs huggingface dataset:
Differential Proteomic Analysis of Rickettsia prowazekii Propagated in Diverse Host Backgrounds

ABSTRACT The obligate intracellular growth of Rickettsia prowazekii places severe restrictions on the analysis of rickettsial gene expression. With a small genome, predicted to code for 835 proteins, identifying which proteins are differentially expressed in rickettsiae that are isolated from different hosts or that vary in virulence is critical to an understanding of rickettsial pathogenicity. We employed a liquid chromatography (LC)-linear trap quadrupole (LTQ)-Orbitrap mass spectrometer for simultaneous acquisition of quantitative mass spectrometry (MS)-only data and tandem mass spectrometry (MS-MS) sequence data. With the use of a combination of commercially available algorithms and in-house software, quantitative MS-only data and comprehensive peptide coverage generated from MS-MS were integrated, resulting in the assignment of peptide identities with intensity values, allowing for the differential comparison of complex protein samples. With the use of these protocols, it was possible to directly compare protein abundance and analyze changes in the total proteome profile of R. prowazekii grown in different host backgrounds. Total protein extracted from rickettsiae grown in murine, tick, and insect cell lines or hen egg yolk sacs was analyzed. Here, we report the fold changes, including an upregulation of shock-related proteins, in rickettsiae cultivated in tissue culture compared to the level for rickettsiae harvested from hen yolk sacs. The ability to directly compare, in a complex sample, differential rickettsial protein expression provides a snapshot of host-specific proteomic profiles that will help to identify proteins important in intracellular growth and virulence.
Spoilage-Related Activity of Carnobacterium maltaromaticum Strains in Air-Stored and Vacuum-Packed Meat

ABSTRACT One hundred three isolates of Carnobacterium spp. from raw meat were analyzed by random amplification of polymorphic DNA (RAPD) and PCR and were identified by 16S rRNA gene sequencing. Forty-five strains of Carnobacterium maltaromaticum were characterized for their growth capabilities at different temperatures, NaCl concentrations, and pH values and for in vitro lipolytic and proteolytic activities. Moreover, their spoilage potential in meat was investigated by analyzing the release of volatile organic compounds (VOCs) in meat stored in air or vacuum packs. Almost all the strains were able to grow at 4, 10, and 20°C, at pH values of 6 to 9, and in the presence of 2.5% NaCl. The release of VOCs by each strain in beef stored at 4°C in air and vacuum packs was evaluated by headspace solid-phase microextraction (HS-SPME)-gas chromatography-mass spectrometry (GC-MS) analysis. All the meat samples inoculated and stored in air showed higher numbers of VOCs than the vacuum-packed meat samples. Acetoin, 1-octen-3-ol, and butanoic acid were the compounds most frequently found under both storage conditions. The contaminated meat samples were evaluated by a sensory panel; the results indicated that for all sensory odors, no effect of strain was significant (P > 0.05). The storage conditions significantly affected (P < 0.05) the perception of dairy, spoiled-meat, and mozzarella cheese odors, which were more intense in meat stored in air than in vacuum packs but were never very intense. In conclusion, different strains of C. maltaromaticum can grow efficiently in meat stored at low temperatures both in air and in vacuum packs, producing volatile molecules with low sensory impacts, with a negligible contribution to meat spoilage overall.
Characterization of Two Distinct Glycosyl Hydrolase Family 78 α-l-Rhamnosidases from Pediococcus acidilactici

ABSTRACT α-l-Rhamnosidases play an important role in the hydrolysis of glycosylated aroma compounds (especially terpenes) from wine. Although several authors have demonstrated the enological importance of fungal rhamnosidases, the information on bacterial enzymes in this context is still limited. In order to fill this important gap, two putative rhamnosidase genes (ram and ram2) from Pediococcus acidilactici DSM 20284 were heterologously expressed, and the respective gene products were characterized. In combination with a bacterial β-glucosidase, both enzymes released the monoterpenes linalool and cis-linalool oxide from a muscat wine extract under ideal conditions. Additionally, Ram could release significant amounts of geraniol and citronellol/nerol. Nevertheless, the potential enological value of these enzymes is limited by the strong negative effects of acidity and ethanol on the activities of Ram and Ram2. Therefore, a direct application in winemaking seems unlikely. Although both enzymes are members of the same glycosyl hydrolase family (GH 78), our results clearly suggest the distinct functionalities of Ram and Ram2, probably representing two subclasses within GH 78: Ram could efficiently hydrolyze only the synthetic substrate p-nitrophenyl-α-l-rhamnopyranoside (V max = 243 U mg−1). In contrast, Ram2 displayed considerable specificity toward hesperidin (V max = 34 U mg−1) and, especially, rutinose (V max = 1,200 U mg−1), a disaccharide composed of glucose and rhamnose. Both enzymes were unable to hydrolyze the flavanone glycoside naringin. Interestingly, both enzymes displayed indications of positive substrate cooperativity. This study presents detailed kinetic data on two novel rhamnosidases, which could be relevant for the further study of bacterial glycosidases.
A system for machine recognition of music patterns

We introduce a system for machine recognition of music patterns. The problem is put into a pattern recognition framework in the sense that an error between a target pattern and scanned pattern is minimized. The error takes into account pitch and rhythm information. The pitch error measure consists of an absolute (objective) error and a perceptual error. The latter depends on an algorithm for establishing the tonal context which is based on Krumhansl's (1990) key-finding algorithm. The sequence of maximum correlations that it outputs is smoothed with a cubic spline and is used to determine weights for perceptual and absolute pitch errors. Maximum correlations are used to create the assigned key sequence, which is then filtered by a recursive median filter to improve the structure of the output of the key finding algorithm. A procedure for choosing weights given to pitch and rhythm errors is discussed.
Active Autotrophic Ammonia-Oxidizing Bacteria in Biofilm Enrichments from Simulated Creek Ecosystems at Two Ammonium Concentrations Respond to Temperature Manipulation

ABSTRACT The first step of nitrification, the oxidation of ammonia to nitrite, is important for reducing eutrophication in freshwater environments when coupled with anammox (anaerobic ammonium oxidation) or denitrification. We analyzed active formerly biofilm-associated aerobic ammonia-oxidizing communities originating from Ammerbach (AS) and Leutra South (LS) stream water (683 ± 550 [mean ± standard deviation] and 16 ± 7 μM NH4 +, respectively) that were developed in a flow-channel experiment and incubated under three temperature regimens. By stable-isotope probing using 13CO2, we found that members of the Bacteria and not Archaea were the functionally dominant autotrophic ammonia oxidizers at all temperatures under relatively high ammonium loads. The copy numbers of bacterial amoA genes in 13C-labeled DNA were lower at 30°C than at 13°C in both stream enrichment cultures. However, the community composition of the ammonia-oxidizing bacteria (AOB) in the 13C-labeled DNA responded differently to temperature manipulation at two ammonium concentrations. In LS enrichments incubated at the in situ temperature (13°C), Nitrosomonas oligotropha-like sequences were retrieved with sequences from Nitrosospira AmoA cluster 4, while the proportion of Nitrosospira sequences increased at higher temperatures. In AS enrichments incubated at 13°C and 20°C, AmoA cluster 4 sequences were dominant; Nitrosomonas nitrosa-like sequences dominated at 30°C. Biofilm-associated AOB communities were affected differentially by temperature at two relatively high ammonium concentrations, implicating them in a potential role in governing contaminated freshwater AOB distributions.
Linear and non-linear filters for block based motion estimation

Many techniques are currently used for motion estimation. In the block-based approaches the most common procedure applied is the block matching based on various algorithms. To refine the motion estimates resulting from the full search or any coarse search algorithm, one can find few applications of Kalman filtering, mainly in the intraframe scheme. This paper presents an 8/spl times/8-block based motion estimation which uses the Kalman filtering technique to improve the motion estimates resulting from both the three step algorithm and the 16/spl times/16-block based Kalman application. In the interframe scheme, due to discontinuities in the dynamic behaviour of the motion vectors, we propose the filtering by approximated densities. This application uses a simple form involving statistical characteristics of multi-modal distributions.
Stable Isotope Probing of an Algal Bloom To Identify Uncultivated Members of the Rhodobacteraceae Associated with Low-Molecular-Weight Polycyclic Aromatic Hydrocarbon Degradation

ABSTRACT Polycyclic aromatic hydrocarbon (PAH)-degrading bacteria associated with an algal bloom in Tampa Bay, FL, were investigated by stable isotope probing (SIP) with uniformly labeled [13C]naphthalene. The dominant sequences in clone libraries constructed from 13C-enriched bacterial DNA (from naphthalene enrichments) were identified as uncharacterized members of the family Rhodobacteraceae. Quantitative PCR primers targeting the 16S rRNA gene of these uncultivated organisms were used to determine their abundance in incubations amended with unlabeled naphthalene and phenanthrene, both of which showed substantial increases in gene copy numbers during the experiments. As demonstrated by this work, the application of uniformly 13C-labeled PAHs in SIP experiments can successfully be used to identify novel PAH-degrading bacteria in marine waters.
Harnessing Defect-Tolerance at the Nanoscale: Highly Luminescent Lead Halide Perovskite Nanocrystals in Mesoporous Silica Matrixes

Colloidal lead halide perovskite nanocrystals (NCs) have recently emerged as a novel class of bright emitters with pure colors spanning the entire visible spectral range. Contrary to conventional quantum dots, such as CdSe and InP NCs, perovskite NCs feature unusual, defect-tolerant photophysics. Specifically, surface dangling bonds and intrinsic point defects such as vacancies do not form midgap states, known to trap carriers and thereby quench photoluminescence (PL). Accordingly, perovskite NCs need not be electronically surface-passivated (with, for instance, ligands and wider-gap materials) and do not noticeably suffer from photo-oxidation. Novel opportunities for their preparation therefore can be envisaged. Herein, we show that the infiltration of perovskite precursor solutions into the pores of mesoporous silica, followed by drying, leads to the template-assisted formation of perovskite NCs. The most striking outcome of this simple methodology is very bright PL with quantum efficiencies exceeding 50%. This facile strategy can be applied to a large variety of perovskite compounds, hybrid and fully inorganic, with the general formula APbX3, where A is cesium (Cs), methylammonium (MA), or formamidinium (FA), and X is Cl, Br, I or a mixture thereof. The luminescent properties of the resulting templated NCs can be tuned by both quantum size effects as well as composition. Also exhibiting intrinsic haze due to scattering within the composite, such materials may find applications as replacements for conventional phosphors in liquid-crystal television display technologies and in related luminescence down-conversion-based devices.
SNR analysis of time-frequency distributions

The SNR analysis has been widely used to evaluate the performance of time-frequency (t-f) distributions. Often the SNR is defined at a specific t-f location or using the averaged variance over the entire t-f domain. In this paper, a new SNR measure is provided based on averaging along the signal t-f signature and its properties for linear FM signals are delineated. It is shown that the SNR increases for increased integration range, and is not highly sensitive to the FM sweeping rate.
Lack of Correlation between Virus Barosensitivity and the Presence of a Viral Envelope during Inactivation of Human Rotavirus, Vesicular Stomatitis Virus, and Avian Metapneumovirus by High-Pressure Processing

ABSTRACT High-pressure processing (HPP) is a nonthermal technology that has been shown to effectively inactivate a wide range of microorganisms. However, the effectiveness of HPP on inactivation of viruses is relatively less well understood. We systematically investigated the effects of intrinsic (pH) and processing (pressure, time, and temperature) parameters on the pressure inactivation of a nonenveloped virus (human rotavirus [HRV]) and two enveloped viruses (vesicular stomatitis virus [VSV] and avian metapneumovirus [aMPV]). We demonstrated that HPP can efficiently inactivate all tested viruses under optimal conditions, although the pressure susceptibilities and the roles of temperature and pH substantially varied among these viruses regardless of the presence of a viral envelope. We found that VSV was much more stable than most food-borne viruses, whereas aMPV was highly susceptible to HPP. When viruses were held for 2 min under 350 MPa at 4°C, 1.1-log, 3.9-log, and 5.0-log virus reductions were achieved for VSV, HRV, and aMPV, respectively. Both VSV and aMPV were more susceptible to HPP at higher temperature and lower pH. In contrast, HRV was more easily inactivated at higher pH, although temperature did not have a significant impact on inactivation. Furthermore, we demonstrated that the damage of virion structure by disruption of the viral envelope and/or capsid is the primary mechanism underlying HPP-induced viral inactivation. In addition, VSV glycoprotein remained antigenic although VSV was completely inactivated. Taken together, our findings suggest that HPP is a promising technology to eliminate viral contaminants in high-risk foods, water, and other fomites.
Aerosol Susceptibility of Influenza Virus to UV-C Light

ABSTRACT The person-to-person transmission of influenza virus, especially in the event of a pandemic caused by a highly virulent strain of influenza, such as H5N1 avian influenza, is of great concern due to widespread mortality and morbidity. The consequences of seasonal influenza are also substantial. Because airborne transmission appears to play a role in the spread of influenza, public health interventions should focus on preventing or interrupting this process. Air disinfection via upper-room 254-nm germicidal UV (UV-C) light in public buildings may be able to reduce influenza transmission via the airborne route. We characterized the susceptibility of influenza A virus (H1N1, PR-8) aerosols to UV-C light using a benchtop chamber equipped with a UVC exposure window. We evaluated virus susceptibility to UV-C doses ranging from 4 to 12 J/m2 at three relative humidity levels (25, 50, and 75%). Our data show that the Z values (susceptibility factors) were higher (more susceptible) to UV-C than what has been reported previously. Furthermore, dose-response plots showed that influenza virus susceptibility increases with decreasing relative humidity. This work provides an essential scientific basis for designing and utilizing effective upper-room UV-C light installations for the prevention of the airborne transmission of influenza by characterizing its susceptibility to UV-C.
Peak current estimation for digital filters

Estimates of the peak power dissipation and the peak current are required in the design of reliable VLSI circuits. The peak current current drawn by a digital filter is dependent on the filter coefficients and the inputs to the multipliers in the filter. This input dependence makes the estimation of peak current for a digital filter a hard problem. We present a technique to estimate the maximum current drawn by a digital filter. The approach consists of: (1) building peak current macro-models for multipliers in terms of the input data transitions and the coefficient, and (2) using these models in a graph based formulation for finding the peak current of the digital filter. The peak current macro-models for multipliers are validated by comparisons with SPICE simulations. We also present the application of the technique for estimating the peak current of digital filters in a 51.84 Mb/s 16-CAP receiver.
A Novel Restriction-Modification System Is Responsible for Temperature-Dependent Phage Resistance in Listeria monocytogenes ECII

ABSTRACT Listeria monocytogenes epidemic clone II (ECII) strains are unusual in being completely resistant to phage when grown at low temperatures (≤30°C). In the current study we constructed and characterized a mariner-based mutant (J46C) of the ECII strain H7550-CdS that lacked temperature-dependent resistance to phage. The transposon was localized in LMOh7858_2753 (open reading frame [ORF] 2753), a member of a 12-ORF genomic island unique to ECII strains. ORF 2753 and ORF 2754 exhibited homologies to restriction endonucleases and methyltransferases associated with type II restriction-modification (RM) systems. In silico-based predictions of the recognition site for this putative RM system were supported by resistance of DNA from ECII strains to digestion by BfuI, a type II restriction enzyme specific for GTATCC (N6/5). Similarly to J46C, a mutant harboring an in-frame deletion of ORF 2753 was susceptible to phage regardless of temperature of growth (25°C or 37°C). Genetic complementation restored phage resistance in 25°C-grown cells of ORF 2753 mutants. Reverse transcription (RT) and quantitative real-time PCR data suggested enhanced transcription of ORF 2753 at low temperatures (≤25°C) compared to 37°C. In contrast, available transcriptional data suggested that the putative methyltransferase (ORF 2754) was constitutively expressed at all tested temperatures (4 to 37°C). Thus, temperature-dependent resistance of L. monocytogenes ECII to phage is mediated by temperature-dependent expression of the restriction endonuclease associated with a novel RM system (LmoH7) unique to this epidemic clone.
Design of Chimeric Levansucrases with Improved Transglycosylation Activity

ABSTRACT Fructansucrases (FSs), including levansucrases and inulosucrases, are enzymes that synthesize fructose polymers from sucrose by the direct transfer of the fructosyl moiety to a growing polymer chain. These enzymes, particularly the single domain fructansucrases, also possess an important hydrolytic activity, which may account for as much as 70 to 80% of substrate conversion, depending on reaction conditions. Here, we report the construction of four chimeric levansucrases from SacB, a single domain levansucrase produced by Bacillus subtilis. Based on observations derived from the effect of domain deletion in both multidomain fructansucrases and glucansucrases, we attached different extensions to SacB. These extensions included the transitional domain and complete C-terminal domain of Leuconostoc citreum inulosucrase (IslA), Leuconostoc mesenteroides levansucrase (LevC), and a L. mesenteroides glucansucrase (DsrP). It was found that in some cases the hydrolytic activity was reduced to less than 10% of substrate conversion; however, all of the constructs were as stable as SacB. This shift in enzyme specificity was observed even when the SacB catalytic domain was extended only with the transitional region found in multidomain FSs. Specific kinetic analysis revealed that this change in specificity of the SacB chimeric constructs was derived from a 5-fold increase in the transfructosylation k cat and not from a reduction of the hydrolytic k cat, which remained constant.
Advance care planning in COPD

Chronic obstructive pulmonary disease (COPD) in advanced stages runs an unpredictable downward course with increasingly frequent, ultimately fatal exacerbations. Worldwide financial and human costs are huge. Responsibility for initiating advance care planning in COPD has usually fallen to the physicians. The tendency has been to avoid this aspect of care, which can result in inadequate, rushed, reactive, crisis decision-making in the form of a “code status” discussion. In this article, I review the relevant literature and report findings from a qualitative study designed within my doctoral program to explore the question, “What is required for meaningful and effective advance care planning in the context of advanced COPD? ” I describe the “collaborative care” approach to advance care planning I used with eight patients and carers living with advanced COPD. Along with a skilled clinician facilitator, user-friendly education elements, and attention to readiness, unique aspects of the approach included a focus on caring, engaging hope, facilitator reflective praxis, and contextual sensitivity. This approach has significant potential for enhancing decision making and goal setting, efficiency of resource utilization, and satisfaction with outcomes. Done well, it may reclaim the care element in advance care planning as it addresses barriers cited by physicians and patients/families.
Fusion of a Novel Genetically Engineered Chitosan Affinity Protein and Green Fluorescent Protein for Specific Detection of Chitosan In Vitro and In Situ

ABSTRACT Chitin is the second most abundant polysaccharide, present, e.g., in insect and arthropod exoskeletons and fungal cell walls. In some species or under specific conditions, chitin appears to be enzymatically de-N-acetylated to chitosan—e.g., when pathogenic fungi invade their host tissues. Here, the deacetylation of chitin is assumed to represent a pathogenicity mechanism protecting the fungus from the host's chitin-driven immune response. While highly specific chitin binding lectins are well known and easily available, this is not the case for chitosan-specific probes. This is partly due to the poor antigenicity of chitosan so that producing high-affinity, specific antibodies is difficult. Also, lectins with specificity to chitosan have been described but are not commercially available, and our attempts to reproduce the findings were not successful. We have, therefore, generated a fusion protein between a chitosanase inactivated by site-directed mutagenesis, the green fluorescent protein (GFP), and StrepII, as well as His6 tags for purification and detection. The recombinant chitosan affinity protein (CAP) expressed in Escherichia coli was shown to specifically bind to chitosan, but not to chitin, and the affinity increased with decreasing degree of acetylation. In vitro, CAP detection was possible either based on GFP fluorescence or using Strep-Tactin conjugates or anti-His5 antibodies. CAP fluorescence microscopy revealed binding to the chitosan exposing endophytic infection structures of the wheat stem rust fungus, but not the chitin exposing ectophytic infection structures, verifying its suitability for in situ chitosan staining.