Miracle-dz/UniFAR-FTUs huggingface dataset:
Expression in Escherichia coli of Native and Chimeric Phenolic Acid Decarboxylases with Modified Enzymatic Activities and Method for Screening Recombinant E. coli Strains Expressing These Enzymes

ABSTRACT Four bacterial phenolic acid decarboxylases (PAD) fromLactobacillus plantarum, Pediococcus pentosaceus, Bacillus subtilis, and Bacillus pumilus were expressed in Escherichia coli, and their activities on p-coumaric, ferulic, and caffeic acids were compared. Although these four enzymes displayed 61% amino acid sequence identity, they exhibit different activities for ferulic and caffeic acid metabolism. To elucidate the domain(s) that determines these differences, chimeric PAD proteins were constructed and expressed in E. coli by exchanging their individual carboxy-terminal portions. Analysis of the chimeric enzyme activities suggests that the C-terminal region may be involved in determining PAD substrate specificity and catalytic capacity. In order to test phenolic acid toxicity, the levels of growth of recombinant E. colidisplaying and not displaying PAD activity were compared on medium supplemented with different concentrations of phenolic acids and with differing pHs. Though these acids already have a slight inhibitory effect on E. coli, vinyl phenol derivatives, created during decarboxylation of phenolic acids, were much more inhibitory to theE. coli control strain. To take advantage of this property, a solid medium with the appropriate pH and phenolic acid concentration was developed; in this medium the recombinant E. colistrains expressing PAD activity form colonies approximately five times smaller than those formed by strains devoid of PAD activity.
Identification of Channel-lining Amino Acid Residues in the Hydrophobic Segment of Colicin Ia

Colicin Ia is a bactericidal protein of 626 amino acid residues that kills its target cell by forming a channel in the inner membrane; it can also form voltage-dependent channels in planar lipid bilayer membranes. The channel-forming activity resides in the carboxy-terminal domain of ∼177 residues. In the crystal structure of the water-soluble conformation, this domain consists of a bundle of 10 α-helices, with eight mostly amphipathic helices surrounding a hydrophobic helical hairpin (helices H8-H9). We wish to know how this structure changes to form a channel in a lipid bilayer. Although there is evidence that the open channel has four transmembrane segments (H8, H9, and parts of H1 and H6-H7), their arrangement relative to the pore is largely unknown. Given the lack of a detailed structural model, it is imperative to better characterize the channel-lining protein segments. Here, we focus on a segment of 44 residues (573–616), which in the crystal structure comprises the H8-H9 hairpin and flanking regions. We mutated each of these residues to a unique cysteine, added the mutant colicins to the cis side of planar bilayers to form channels, and determined whether sulfhydryl-specific methanethiosulfonate reagents could alter the conduction of ions through the open channel. We found a pattern of reactivity consistent with parts of H8 and H9 lining the channel as α-helices, albeit rather short ones for spanning a lipid bilayer (12 residues). The effects of the reactions on channel conductance and selectivity tend to be greater for residues near the amino terminus of H8 and the carboxy terminus of H9, with particularly large effects for G577C, T581C, and G609C, suggesting that these residues may occupy a relatively constricted region near the cis end of the channel.
Human leukocyte antigen crossmatch testing is important for liver retransplantation

Although human leukocyte antigen (HLA) crossmatching is often thought to be unnecessary for liver transplants (LTs), we provide evidence that for retransplants, it is essential. Sera from 139 retransplant patients who had received livers from deceased donors were retrospectively analyzed with single antigen beads on a Luminex platform for HLA antibodies. Each patient received at least 2 transplants and was followed up for at least 6 months from the second LT, which was deemed to have failed if the patient had a third LT or died. Second LT survival was calculated from the date of the second LT to the date of the third LT or death. Our study cohort consisted of 118 adult patients (≥18 years old) as well as 21 pediatric patients (<18 years old). Class I HLA antibodies were associated with significantly poorer regraft survival in adults [survival differences of 21.3% (P = 0.046), 22.1% (P = 0.042), and 23.7% (P = 0.033) at 1, 3, and 5 years, respectively]; however, the presence of these antibodies was not associated with significant survival differences in the pediatric population. A univariate analysis of the effect of class I antibodies on second LT survival in adults showed a hazard ratio of 2.0 (95% confidence interval = 1.0‐3.8, P = 0.028). Graft survival in patients with and without HLA antibodies or class II antibodies was similar. Because class I antibodies have a deleterious effect on liver regraft survival, crossmatch testing should be performed before liver retransplantation. Liver Transpl 16:308–313, 2010. © 2010 AASLD.
Reduced plasma concentrations of vitamin B6 and increased plasma concentrations of the neurotoxin 3-hydroxykynurenine are associated with nodding syndrome: a case control study in Gulu and Amuru districts, Northern Uganda

Introduction Nodding syndrome was first reported in Uganda in 2003 among internally displaced populations. Risk factors for the syndrome remain unknown. We therefore explored vitamin B6 deficiency and resulting high 3-hydroxykynurenine (3-HK) levels as risk factor for nodding syndrome in Northern Uganda. Methods Case-control study conducted in Gulu and Amuru districts. Cases were children/young adults with nodding syndrome. Healthy children/young adults were recruited as controls from same community as cases. Data on socio-demographic and other risk factors was collected using questionnaires. Whole blood was collected in EDTA tubes for assay of 3-HK and vitamin B6 using sandwich ELISA. Conditional logistic regression model was used to assess associations. Results 66 cases and 73 controls were studied. Factors associated with nodding syndrome were being positive for 3-HK (AOR=4.50, p=0.013), vitamin B6 concentration below mean (AOR=7.22, P=0.001), child being taken care of by mother only (AOR=5.43, p=0.011), child being taken care of by guardian (AOR=5.90, p=0.019) and child consuming relief food at weaning (AOR=4.05, p=0.021). Conclusion Having low vitamin B6 concentration which leads to a build up of 3-hydroxykynurenine concentration in cases as a main risk factor. Therefore, cases should be treated with vitamin B6 and community members should be sensitise to ensure adequate dietary intake of vitamin B6 so that the risk of nodding syndrome among children is averted. We encourage future prospective intervention study to be conducted to assess the effect of low vitamin B6 on the development of nodding syndrome via raised 3-HK concentration.
Persistence of four related human immunodeficiency virus subtypes during the course of zidovudine therapy: relationship between virion RNA and proviral DNA

Human immunodeficiency virus (HIV) virion RNA and proviral DNA sequences have been examined over a 1-year period in an HIV-seropositive patient, commencing with the start of zidovudine treatment. By characterizing the variable V3 and V4 env domains, four related but structurally discrete genotypes could be identified prior to the start of therapy and during the subsequent 60-week period of therapy. Each of the four subtypes showed a unique pattern in the preservation of glycosylation sites. A comparison of the V3 amino acid sequences in peripheral blood mononuclear cell proviral DNA and plasma virion RNA at 0, 24, 36, and 60 weeks demonstrated that proviral DNA did not serve as a predictor of the structure of virion RNA. HIV virion RNA subtype 3 was the most prevalent virion RNA subtype at three of the four periods studied, yet no corresponding proviral DNA was detected. Other virion subtypes have been observed, but only on a transient basis. The present data are consistent with a model of HIV infection in which related but different HIV substrains coexist and evolve independently within an individual. Characterization of virion RNA may be required to identify the unique properties of the virus involved in disease progression; characterization of proviral DNA will not yield this information.
CONSTRUCTING PARTICIPATORY JOURNALISM AS A SCHOLARLY OBJECT

In this article, we investigate the emergence of “participatory journalism” as a scholarly object in the field of journalism studies. By conducting a genealogical analysis of 119 articles on participatory journalism, published between 1995 and September 2011, we analyze the development of scholarly ways of writing and thinking about participatory journalism over the years. Our genealogy reveals how the field of journalism studies constructs participatory journalism along the lines of four normative dimensions: “enthusiasm about new democratic opportunities”, “disappointment with professional journalism’s obduracy”, “disappointment with economic motives to facilitate participatory journalism”, and “disappointment with news users' passivity”. We argue these dimensions are inextricably linked with what “counts” as journalism within journalism studies.
Optimality of diagonalization of multi-hop MIMO relays

For a two-hop linear non-regenerative multiple-input multiple-output (MIMO) relay system where the direct link between source and destination is negligible, the optimal design of the source and relay matrices has been recently established for a broad class of objective functions. The optimal source and relay matrices jointly diagonalize the MIMO relay system into a set of parallel scalar channels. In this paper, we show that this diagonalization is also optimal for a multihop MIMO relay system with any number of hops, which is a further generalization of several previously established results. Specifically, for Schur-concave objective functions, the optimal source precoding matrix, the optimal relay amplifying matrices and the optimal receiving matrix jointly diagonalize the multihop MIMO relay channel. And for Schur-convex objectives, such joint diagonalization along with a rotation of the source precoding matrix is also shown to be optimal. We also analyze the system performance when each node has the same transmission power budget and the same asymptotically large number of antennas. The asymptotic analysis shows a good agreement with numerical results under a finite number of antennas.
Validating a screening questionnaire for parkinsonism in Australia

Parkinson's disease is a common neurodegenerative disorder in elderly people. Epidemiological studies of the disease can be labour intensive. A two phase design including a screening questionnaire as the first phase has become a popular method in prevalence studies of Parkinson's disease. Such a design has many advantages including less work for assessing physicians and enhanced recruitment of people to be screened. However, its wider application may be questioned because validation has been limited to samples that are drawn from hospitals (or clinics) and may be inappropriate for a community setting. This study assesses whether validating screening questionnaire by using a hospital sample yields the same result as a community based sample. Furthermore, it seeks to establish whether the screening instrument can be simplified to involve less questions. The findings show that some of the questions used in the screening phase yield different responses when comparing a hospital group with a community group. This study also provides a simplified model of questions that may be relevant for screening in the community setting.
Comparison of In Vitro Antifungal Activities of Free and Liposome-Encapsulated Nystatin with Those of Four Amphotericin B Formulations

ABSTRACT The in vitro activity of a multilamellar liposomal formulation of nystatin (Nyotran) was compared with those of free nystatin and four pharmaceutical preparations of amphotericin B. MICs for 200 isolates of two Aspergillus spp. , seven Candidaspp. , and Cryptococcus neoformans were determined by a broth microdilution adaptation of the method recommended by the National Committee for Clinical Laboratory Standards. Minimum lethal concentrations (MLCs) of the six antifungal preparations were also determined. Both nystatin formulations possessed fungistatic and fungicidal activities against the 10 species tested. Liposomal nystatin appeared to be as active as free nystatin, with MICs and MLCs that were similar to, or lower than, those of the latter. Neither formulation of nystatin was as active as amphotericin B deoxycholate (Fungizone) or amphotericin B lipid complex (Abelcet), but both were more effective than liposomal amphotericin B (AmBisome). Our results suggest that further evaluation of liposomal nystatin is justified.
Monooxygenase, a Novel Beta-Cypermethrin Degrading Enzyme from Streptomyces sp

The widely used insecticide beta-cypermethrin has become a public concern because of its environmental contamination and toxic effects on mammals. In this study, a novel beta-cypermethrin degrading enzyme designated as CMO was purified to apparent homogeneity from a Streptomyces sp. isolate capable of utilizing beta-cypermethrin as a growth substrate. The native enzyme showed a monomeric structure with a molecular mass of 41 kDa and pI of 5.4. The enzyme exhibited the maximal activity at pH 7.5 and 30°C. It was fairly stable in the pH range from 6.5–8.5 and at temperatures below 10°C. The enzyme activity was significantly stimulated by Fe2+, but strongly inhibited by Ag+, Al3+, and Cu2+. The enzyme catalyzed the degradation of beta-cypermethrin to form five products via hydroxylation and diaryl cleavage. A novel beta-cypermethrin detoxification pathway was proposed based on analysis of these products. The purified enzyme was identified as a monooxygenase by matrix-assisted laser desorption/ionization time-of-flight/time-of-flight mass spectrometry analysis (MALDI-TOF-MS) and N-terminal protein sequencing. Given that all the characterized pyrethroid-degrading enzymes are the members of hydrolase family, CMO represents the first pyrethroid-degrading monooxygenase identified from environmental microorganisms. Taken together, our findings depict a novel pyrethroid degradation mechanism and indicate that the purified enzyme may be a promising candidate for detoxification of beta-cypermethrin and environmental protection.
Accelerometer-based transportation mode detection on smartphones

We present novel accelerometer-based techniques for accurate and fine-grained detection of transportation modes on smartphones. The primary contributions of our work are an improved algorithm for estimating the gravity component of accelerometer measurements, a novel set of accelerometer features that are able to capture key characteristics of vehicular movement patterns, and a hierarchical decomposition of the detection task. We evaluate our approach using over 150 hours of transportation data, which has been collected from 4 different countries and 16 individuals. Results of the evaluation demonstrate that our approach is able to improve transportation mode detection by over 20% compared to current accelerometer-based systems, while at the same time improving generalization and robustness of the detection. The main performance improvements are obtained for motorised transportation modalities, which currently represent the main challenge for smartphone-based transportation mode detection.
Association of the polymorphism Y402H in the CFH gene with response to anti‐VEGF treatment in age‐related macular degeneration: a systematic review and meta‐analysis

To explore whether the complement factor H (CFH) polymorphism rs1061170/Y402H is associated with responsiveness to antivascular endothelial growth factor (VEGF) agents in age‐related macular degeneration (AMD). We reviewed the English literature to examine the association between the polymorphism rs1061170/Y402H of the CFH gene and responsiveness to treatment with anti‐VEGF drugs in AMD patients. A meta‐analysis of eligible studies was also performed. Pooled odds ratios (ORs) and 95% CIs were estimated using Stata V.12. 0. Statistical heterogeneity was measured using Q‐statistic testing. Fourteen relevant studies including a total of 2963 AMD patients were eligible. In AMD patients without a treatment history, individuals carrying the rs1061170/Y402H TT genotype were more likely to achieve a better outcome (OR = 1.932, 95% CI = 1.125–3.317, p = 0.017) than those carrying the CC genotype. The polymorphism rs1061170/Y402H might be a genetic predictor of treatment response to anti‐VEGF therapy in AMD patients. Further prospective research including a larger number of patients is needed to validate this finding.
Stochastic Dynamics of Proteins and the Action of Biological Molecular Machines

It is now well established that most if not all enzymatic proteins display a slow stochastic dynamics of transitions between a variety of conformational substates composing their native state. A hypothesis is stated that the protein conformational transition networks, as just as higher-level biological networks, the protein interaction network, and the metabolic network, have evolved in the process of self-organized criticality. Here, the criticality means that all the three classes of networks are scale-free and, moreover, display a transition from the fractal organization on a small length-scale to the small-world organization on the large length-scale. Good mathematical models of such networks are stochastic critical branching trees extended by long-range shortcuts. Biological molecular machines are proteins that operate under isothermal conditions and hence are referred to as free energy transducers. They can be formally considered as enzymes that simultaneously catalyze two chemical reactions: the free energy-donating (input) reaction and the free energy-accepting (output) one. The far-from-equilibrium degree of coupling between the output and the input reaction fluxes have been studied both theoretically and by means of the Monte Carlo simulations on model networks. For single input and output gates the degree of coupling cannot exceed unity. Study simulations of random walks on model networks involving more extended gates indicate that the case of the degree of coupling value higher than one is realized on the mentioned above critical branching trees extended by long-range shortcuts.
On social networks and collaborative recommendation

Social network systems, like last.fm, play a significant role in Web 2.0, containing large amounts of multimedia-enriched data that are enhanced both by explicit user-provided annotations and implicit aggregated feedback describing the personal preferences of each user. It is also a common tendency for these systems to encourage the creation of virtual networks among their users by allowing them to establish bonds of friendship and thus provide a novel and direct medium for the exchange of data. We investigate the role of these additional relationships in developing a track recommendation system. Taking into account both the social annotation and friendships inherent in the social graph established among users, items and tags, we created a collaborative recommendation system that effectively adapts to the personal information needs of each user. We adopt the generic framework of Random Walk with Restarts in order to provide with a more natural and efficient way to represent social networks. In this work we collected a representative enough portion of the music social network last.fm, capturing explicitly expressed bonds of friendship of the user as well as social tags. We performed a series of comparison experiments between the Random Walk with Restarts model and a user-based collaborative filtering method using the Pearson Correlation similarity. The results show that the graph model system benefits from the additional information embedded in social knowledge. In addition, the graph model outperforms the standard collaborative filtering method.
Live Donor Champion: Finding Live Kidney Donors by Separating the Advocate From the Patient

Background Lack of education and reluctance to initiate a conversation about live donor kidney transplantation is a common barrier to finding a donor. Although transplant candidates are often hesitant to discuss their illness, friends or family members are often eager to spread awareness and are empowered by advocating for the candidates. We hypothesized that separating the advocate from the patient is important in identifying live donors. Methods We developed an intervention to train a live donor champion (LDC; a friend, family member, or community member willing to advocate for the candidate) for this advocacy role. We compared outcomes of 15 adult kidney transplant candidates who had no prospective donors and underwent the LDC intervention with 15 matched controls from our waiting list. Results Comfort in initiating a conversation about transplantation increased over time for LDCs. Twenty-five potential donors contacted our center on behalf of LDC participants; four participants achieved live donor kidney transplantation and three additional participants have donors in evaluation, compared with zero among matched controls (P < 0.001). Conclusions Transplant candidates are ill equipped to seek live donors; by separating the advocate from the patient, understandable concerns about initiating conversations are reduced.
Effectiveness of Omalizumab in a Patient with Severe Asthma, Low Serum IgE Level, and Lack of Sensitized Allergens Induced by Oral Steroid Therapy: The Usefulness of Impulse Oscillation for Assessment of Omalizumab Therapy

Background. Omalizumab is a humanized monoclonal anti-IgE antibody that was recently approved for the treatment of severe allergic asthma. However, omalizumab is not licensed for allergic asthma in patients with a low serum IgE level (<30 IU/mL) or negative results for specific allergen tests. Case history. We present a patient with severe asthma and low serum IgE levels who had negative results for specific allergens induced by oral steroid therapy. Omalizumab administration improved asthma exacerbated forced expiratory volume in 1 s (FEV1) and respiratory resistance measurements based on the impulse oscillation technique (Mostgraph-01). The response to omalizumab therapy was evidenced by a decrease in airway resistance at 1 month. Conclusions. The findings of this case report indicate that omalizumab treatment had beneficial effects in a patient with severe asthma and low total serum IgE levels with negative results for specific IgE, which may have been induced by long-term corticosteroid administration.