Miracle-dz/UniFAR-FTUs huggingface dataset:
Chlorocatechols Substituted at Positions 4 and 5 Are Substrates of the Broad-Spectrum Chlorocatechol 1,2-Dioxygenase of Pseudomonas chlororaphis RW71

ABSTRACT The nucleotide sequence of a 10,528-bp region comprising the chlorocatechol pathway gene cluster tetRtetCDEF of the 1,2,3,4-tetrachlorobenzene via the tetrachlorocatechol-mineralizing bacterium Pseudomonas chlororaphis RW71 (T. Potrawfke, K. N. Timmis, and R.-M. Wittich, Appl. Environ. Microbiol. 64:3798–3806, 1998) was analyzed. The chlorocatechol 1,2-dioxygenase gene tetC was cloned and overexpressed inEscherichia coli. The recombinant gene product was purified, and the α,α-homodimeric TetC was characterized. Electron paramagnetic resonance measurements confirmed the presence of a high-spin-state Fe(III) atom per monomer in the holoprotein. The productive transformation by purified TetC of chlorocatechols bearing chlorine atoms in positions 4 and 5 provided strong evidence for a significantly broadened substrate spectrum of this dioxygenase compared with other chlorocatechol dioxygenases. The conversion of 4,5-dichloro- or tetrachlorocatechol, in the presence of catechol, displayed strong competitive inhibition of catechol turnover. 3-Chlorocatechol, however, was simultaneously transformed, with a rate similar to that of the 4,5-halogenated catechols, indicating similar specificity constants. These novel characteristics of TetC thus differ significantly from results obtained from hitherto analyzed catechol 1,2-dioxygenases and chlorocatechol 1,2-dioxygenases.
Filament and Flare Detection in Hα image sequences

Solar storms can have a major impact on the infrastructure of the earth. Some of the causing events are observable from ground in the H{\alpha} spectral line. In this paper we propose a new method for the simultaneous detection of flares and filaments in H{\alpha} image sequences. Therefore we perform several preprocessing steps to enhance and normalize the images. Based on the intensity values we segment the image by a variational approach. In a final postprecessing step we derive essential properties to classify the events and further demonstrate the performance by comparing our obtained results to the data annotated by an expert. The information produced by our method can be used for near real-time alerts and the statistical analysis of existing data by solar physicists.
Input reduction in human sensation modeling using independent component analysis

We model human sensations in virtual reality applications using cascade neural networks. In the modeling process, the dimension of inputs presented to the humans and the sensation systems may be very high. In this research we propose using the independent component analysis (ICA) to achieve input reduction. We obtain human sensation data from a full-body motion virtual reality interface - "motion-based movie". A fixed-point ICA algorithm is applied to achieve feature extraction and input selection for reducing the dimension of the environmental stimulus data. The fidelity of the sensation models trained using the reduced inputs is verified by the hidden Markov model based similarity measure. The performance of input reduction using ICA is compared with that using the principal component analysis. Experimental results showed that the input selection scheme based on ICA is capable of improving the modeling performance of the computational sensation systems and reducing the input dimension by 60%.
Peak in matrix metaloproteinases-2 levels observed during recovery from olfactory nerve injury

Matrix metalloproteineases are associated with extracellular remodeling that occurs in injury and repair processes in the central nervous system (CNS). We examined the role of MMP-2 in a model of olfactory nerve injury and found that MMP-2 levels increased several hours following injury, peaked at day 7 and then decreased rapidly. We previously reported a rapid increase in MMP-9, within 5 h after nerve injury, corresponding to neuronal degeneration and increased glial activity. In this study, we show that MMP-2 peaks later than MMP-9, at the onset of neuronal regeneration and repair. Using MMP-9 knockout mice, we determined that the MMP-2 increase is independent of MMP-9. Our data suggest that MMP-2 and MMP-9 may play different roles in the injury and repair processes.
Nonviral Gene Delivery: Principle, Limitations, and Recent Progress

Gene therapy is becoming a promising therapeutic modality for the treatment of genetic and acquired disorders. Nonviral approaches as alternative gene transfer vehicles to the popular viral vectors have received significant attention because of their favorable properties, including lack of immunogenicity, low toxicity, and potential for tissue specificity. Such approaches have been tested in preclinical studies and human clinical trials over the last decade. Although therapeutic benefit has been demonstrated in animal models, gene delivery efficiency of the nonviral approaches remains to be a key obstacle for clinical applications. This review focuses on existing and emerging concepts of chemical and physical methods for delivery of therapeutic nucleic acid molecules in vivo. The emphasis is placed on discussion about problems associated with current nonviral methods and recent efforts toward refinement of nonviral approaches.
Heterogeneous Architectures For Parallel Acceleration

To enable a new generation of digital computing applications, the greatest challenge is to provide a better level of energy efficiency (intended as the performance that a system can provide within a certain power budget) without giving up a systems's flexibility. This constraint applies to digital system across all scales, starting from ultra-low power implanted devices up to datacenters for high-performance computing and for the "cloud". In this thesis, we show that architectural heterogeneity is the key to provide this efficiency and to respond to many of the challenges of tomorrow's computer architecture - and at the same time we show methodologies to introduce it with little or no loss in terms of flexibility. In particular, we show that heterogeneity can be employed to tackle the "walls" that impede further development of new computing applications: the utilization wall, i.e. the impossibility to keep all transistors on in deeply integrated chips, and the "data deluge", i.e. the amount of data to be processed that is scaling up much faster than the computing performance and efficiency. We introduce a methodology to improve heterogeneous design exploration of tightly coupled clusters; moreover we propose a fractal heterogeneity architecture that is a parallel accelerator for low-power sensor nodes, and is itself internally heterogeneous thanks to an heterogeneous coprocessor for brain-inspired computing. This platform, which is silicon-proven, can lead to more than 100x improvement in terms of energy efficiency with respect to typical computing nodes used within the same domain, enabling the application of complex algorithms, vastly more performance-hungry than the current state-of-the-art in the ULP computing domain.
A Single-Chain Class II MHC-IgG3 Fusion Protein Inhibits Autoimmune Arthritis by Induction of Antigen-Specific Hyporesponsiveness1

T cells play a central role in many autoimmune diseases. A method to specifically target the function of autoreactive T cell clones would avoid the global immunosuppression associated with current therapies. To develop a molecule capable of inhibiting autoreactive T cell responses in vivo, single-chain peptide-I-A-IgG3 fusion proteins were constructed and expressed in both mammalian and insect cells. The fusion proteins were designed with an IgG3 Fc moiety to make them divalent, allowing TCR cross-linking, while lacking FcR binding and costimulation. The fusion proteins stimulated T cell hybridomas in vitro in a peptide-specific, MHC-restricted manner but failed to do so in soluble form. In vivo administration of an I-Aq fusion protein, containing an immunodominant collagen II peptide, significantly delayed the onset and reduced the severity of collagen-induced arthritis in DBA/1 mice by induction of Ag-specific hyporesponsiveness. Such fusion proteins may be useful to study novel therapeutic approaches for T cell-mediated autoimmune diseases.
Integrating the Functional Encryption and Proxy Re-cryptography to Secure DRM Scheme

The current Digital Rights Management (DRM) systems use attribute-based encryption (ABE) and proxy re-encryption (PRE) to achieve fine-grained access control in cloud computing. However, these schemes have some limitations particularly in terms of security, functionality and also higher decryption time which grows linearly with the complexity of access policies. In this paper, we propose a novel DRM scheme founded on a deterministic finite automata-based functional proxy re-encryption (DFA-based FPRE) scheme which has been proven to be secure against CCA in the standard model. In particular, we leverage the DFA-based FPRE scheme to realize fine-grained access control over encrypted contents among a set of users. Furthermore, a secure content key distribution protocol and efficient revocation mechanism are provided. Moreover, we tackle the critical issue of high computation at the user side, by outsourcing computation into (DFA-based FPRE) scheme for the first time. In comparison, our scheme achieves higher efficiency and smaller computation time against state-of-the-art.
Can computers help in assessing children's postoperative pain? Initial validation of a computer-assisted interview.

BACKGROUND AND OBJECTIVE Computers offer the potential for the assessment of children who have difficulties in communication and cannot describe pain using conventional approaches. Such approaches must be reliable and valid. As a preliminary step towards this goal, the validity and reliability of a computer-assisted pain assessment for children (MacInterview) was assessed using children with no known disabilities who had undergone surgery. METHODS MacInterview uses body outlines and a range of different pain representations with scaling for size and intensity, and associated emotion. Following piloting with non-clinic children, the experience of acute postoperative pain was assessed for 30 children undergoing adenotonsillectomy or tonsillectomy the day following surgery using the MacInterview and three existing standardized assessment measures. Each child self-reported their current experience of postoperative pain on two occasions 30 min apart, and retrospectively on pain the previous evening in the immediate postoperative period. RESULTS Analyses indicated good performance of MacInterview, showing positive correlations between 0.65 and 0.88 with standardized pain-intensity measures, and test-retest reliability was 0.9. Face validity was high, and children enjoyed the procedure. CONCLUSIONS The procedure shows promise and is likely to merit further development for children showing difficulties in communication.
Perceptions of contraception, non-protection and induced abortion among a sample of urban Swedish teenage girls: Focus group discussions

Objectives To explore the attitudes of teenage girls towards contraception and induced abortion in order to better understand underlying reasons for non-protection. Methods Four focus group discussions with urban teenage girls aged 15–18 years (n = 16). Results Attitudes towards abortion were generally positive despite some degree of misinformation and lack of knowledge about the subject. Knowledge about methods of birth control was accurate. The use of alcohol was often cited as a factor contributing to risk-taking behaviour. Sexual abuse was mentioned as a common phenomenon, and all participants knew someone who had been sexually abused. Participants agreed that sexual partners were reluctant to use condoms and that it was difficult to negotiate with them about this use. The increased rate of abortion was felt to be mainly due to initiation of sexual activity at a younger age. A need for easily available and inexpensive contraception was expressed along with improvement in the quality of sexual education in school. Conclusion Qualitative sexual education with single-sex sessions and gender related messages as a recurrent activity in the school curricula may help to empower young women and promote avoidance of risk-taking during sexual activity thus helping to reduce the incidence of unwanted pregnancies. In addition, access to cheap condoms could provide a stimulus to increased use of condoms.
Regional brain variations of cytochrome oxidase activity and motor coordination in hot‐foot mutant mice

Hot‐foot mutant mice are characterized by defective arborization of Purkinje cell dendrites, resulting in ataxia of gait and deficits of equilibrium. Regional brain variations of cytochrome oxidase (CO) activity were analysed for the purpose of identifying those brain regions with abnormal metabolic activity as a secondary consequence to the cerebellar alteration. In addition, the possible relation between CO activity and motor deficits was evaluated. By comparison to normal littermate controls of the same background strain, hot‐foot mutants had higher CO activity in the molecular layer of the cerebellum, the ventrolateral and midline thalamic nuclei, as well as in the frontal eye field. There was no other alteration of CO activity in the hot‐foot brain. No linear correlation was discerned between CO activity in the molecular layer of the cerebellum and the ventrolateral and midline nuclei on one hand, and motor coordination performance on the other. These results indicate regionally selective abnormalities of metabolic activity in a cerebellar mutant with defective dendritic arborization of the Purkinje cell.
Field-Dependent Resonant Behavior of Thin Nickel Film-Coated Microcantilever

Herein we describe the vibration of a thin nickel film-coated microcantilever at resonance under an external magnetic field. The resonance frequency and the mechanical loss—experimentally observed while varying the magnetic field—closely follow the field-dependence of the magnetostriction coefficient, indicating the strong coupling between the mechanical motion and the magnetostriction through the surface stress. Comparing to the surface stress model based on uniformly distributed axial load, the magnetostriction coefficient of a nickel film has been estimated, and its value is comparable to the reported one. Our study suggests that the nature of the surface stress originating from the magnetostrictive film can govern and modulate the resonant behavior of miniaturized mechanical systems.
Does the availability of therapeutic drug monitoring, computerised dose recommendation and prescribing decision support services promote compliance with national gentamicin prescribing guidelines?

Gentamicin is an aminoglycoside antibiotic that is highly effective in treating Gram‐negative infections, but inappropriate use leads to toxicity. In 2010, the Australian Therapeutic Guidelines (Antibiotic) were revised to recommend the use of computerised methods to individualise dosing of gentamicin and optimise therapy, rather than traditional nomogram approaches.
Research data management and libraries: Current activities and future priorities

This paper reports research carried out at the end of 2012 to survey UK universities to understand in detail the ways in which libraries are currently involved in research data management and the extent to which the development of research data management services is a strategic priority for them. The research shows that libraries were offering limited research data management services, with highest levels of activity in large research-intensive institutions. There were major challenges associated with skills gaps, resourcing and cultural change. However, libraries are currently involved in developing new institutional research data management policies and services, and see this as an important part of their future role. Priorities such as provision of research data management advisory and training services are emerging. A systematic comparison between these results and other recent studies is made in order to create a full picture of activities and trends. An innovation hype-cycle framework is deployed to understand possible futures and Abbott’s theory of professions is used to gain an insight into how libraries are competing to extend their jurisdiction whilst at the same time working collaboratively with other stakeholders.
Synthesis, Spectroscopy and Electrochemistry of New 3-(5-Aryl-4,5-Dihydro-1H-Pyrazol-3-yl)-4-Hydroxy-2H-Chromene-2-One 4, 5 as a Novel Class of Potential Antibacterial and Antioxidant Derivatives

3-((2E)-3(aryl)prop-2-enoyl)-2H-chromen-2-one 3 was synthesized from 4-hydroxy coumarin by refluxing 3-acetyl-4-hydroxy coumarin with aromatic aldehydes in chloroform in the presence of a catalytic amount of piperidine. 3 was converted to pyrazoles 4, 5 by treatment with hydrazine and phenylhydrazine in toluene, respectively. The structures of the new compounds were confirmed by elemental analysis, IR, and multinuclear/multidimensional NMR spectroscopy (1H, 13C-NMR, NOESY, HMBC) which allowed us to assign the complete network of proton and carbon atoms. All the compounds exhibited one quasireversible redox process. All the newly synthesized compounds were screened for their antibacterial and antioxidant activities. Antimicrobial studies revealed that 3-(5-(2,5-dimethylphenyl)-1-phenyl-4,5-dihydro-1H-pyrazol-3-yl)-4- hydroxy-2H-chromene-2-one 5c showed significant antibacterial activity against Escherichia coli and Pseudomonas Aeruginosa 27853. Furthermore, 3-(5-(aryl)-4,5-dihydro-1H-pyrazol-3-yl)-4-hydroxy-2H-chromene- 2-ones 4, 5 showed antioxidant activities of different extents with respect to individual compounds as well as to the antioxidant methods. The 3-(5-(phenyl)-4,5-dihydro-1H-pyrazol-3-yl)-4-hydroxy-2H-chromene-2-ones 4a was found to be the most active antioxidant in the series and more active than trolox which makes the investigated complexes a new promising class of antibacterial compounds.
The Human Papillomavirus Type 16 E7 Oncogene Is Required for the Productive Stage of the Viral Life Cycle

ABSTRACT The production of the human papillomavirus type 16 (HPV-16) is intimately tied to the differentiation of the host epithelium that it infects. Infection occurs in the basal layer of the epithelium at a site of wounding, where the virus utilizes the host DNA replication machinery to establish itself as a low-copy-number episome. The productive stage of the HPV-16 life cycle occurs in the postmitotic suprabasal layers of the epithelium, where the virus amplifies its DNA to high copy number, synthesizes the capsid proteins (L1 and L2), encapsidates the HPV-16 genome, and releases virion particles as the upper layer of the epithelium is shed. Papillomaviruses are hypothesized to possess a mechanism to overcome the block in DNA synthesis that occurs in the differentiated epithelial cells, and the HPV-16 E7 oncoprotein has been suggested to play a role in this process. To determine whether E7 plays a role in the HPV-16 life cycle, an E7-deficient HPV-16 genome was created by inserting a translational termination linker (TTL) in the E7 gene of the full HPV-16 genome. This DNA was transfected into an immortalized human foreskin keratinocyte cell line shown previously to support the HPV-16 life cycle, and stable cell lines were obtained that harbored the E7-deficient HPV-16 genome episomally, the state of the genome found in normal infections. By culturing these cells under conditions which promote the differentiation of epithelial cells, we found E7 to be necessary for the productive stage of the HPV-16 life cycle. HPV-16 lacking E7 failed to amplify its DNA and expressed reduced amounts of the capsid protein L1, which is required for virus production. E7 appears to create a favorable environment for HPV-16 DNA synthesis by perturbing the keratinocyte differentiation program and inducing the host DNA replication machinery. These data demonstrate that E7 plays an essential role in the papillomavirus life cycle.
Does the sedation regimen affect adverse events during procedural sedation and analgesia in injection drug users?

OBJECTIVES Injection drug users (IDUs) often undergo procedural sedation and analgesia (PSA) as part of emergency department (ED) treatment. We compared adverse events (AEs) using a variety of sedation regimens. METHODS This was a retrospective analysis of a PSA safety audit in two urban EDs. Consecutive self-reported IDUs were identified, and structured data describing comorbidities, vital signs, sedation regimens (propofol [P], propofol-fentanyl [PF], fentanyl-midazolam [FM], ketofol [1:1 ketamine:propofol, KF], and ketamine-propofol [KP]) and AEs were collected. The primary outcome was the proportion of patients in each sedation group having an AE; the secondary outcome was the proportion of patients having a cardiovascular or respiratory AE. RESULTS Data were collected on 276 IDUs (78 P, 82 PF, 65 FM, 25 KF, and 26 KP), and 18 patients had AEs (6.5%, 95% CI 4.0-10.3). The AE rates were 0.0%, 8.5%, 9.2%, 12.0%, and 7.6%, respectively, with propofol having a significantly lower rate (Pearson coefficient 14.9, p = 0.007). The cardiovascular/respiratory AE rates were significantly different as well, with P, KP, and KF having the lowest rates (Pearson coefficient 13.3, p = 0.01). CONCLUSIONS For IDU PSA, the overall AE rate was 6.5%, and propofol appeared to have a significantly lower rate.
Development of forelimb bones in indigenous sheep fetuses.

The study included detection of the sites of ossification centers and their sequence of appearance in the forelimb bones of indigenous sheep fetuses by using double staining method with younger specimens and radiography or maceration methods with old specimens, as well as, histological study with some ages. The results showed that the primary ossification centers of the forelimb in indigenous sheep fetuses appeared firstly in the diaphyses of radius and ulna, humerus, scapula, metacarpus, phalanges and lastly in the carpal bone at an estimated age of 43, 45, 46, 47, 49 - 56 and 90-118 days old respectively. The results of statistical analysis of the total lengths of scapula, humerus, radius, ulna and metacarpus with the lengths of their ossified parts through the 7 th – 15 th weeks of fetus age, showed presence of significant differences in the average of these measurements among most of studied weeks. Also there was a significant differences in the average of relative increase in the total length and length of ossified part of diaphysis of studied bones during the 7 th week in comparison to the same average in the other studied weeks (8 th -15 th week) of indigenous sheep fetuses age.
Who Is Visible: Resolving Access Policy Conflicts in Online Social Networks

Millions of the co-owned items, such as photos, comments etc., are uploaded to OSNs everyday. These co-owned items contain plenty of privacy information. One important information is the social relations which can be inferred from the items. When sharing these items, the owners may just want to make themselves visible alone while hiding these social relations. It leaves us a problem that making each single co-owner visible alone is acceptable, but showing them together is not allowed. To avoid the privacy leakage, we should choose proper owners to be visible to the visitor. Unfortunately, traditional access control for OSNs cannot fit this concern thus cannot provide a suitable answer. To deal with this problem, we first define the `dislike relation' and its corresponding conflicts. Then we propose a communication-intensity-based scheme to measure the social intimacies between the visitor and co-owners of the accessed item. Based on the social intimacies, we can provide a decision support when conflicts occur. Case studies and user studies are performed to illustrate the effectiveness of our proposed scheme.