Miracle-dz/UniFAR-FTUs huggingface dataset:
Crystallization and preliminary X‐ray studies of ornithine decarboxylase from Trypanosoma brucei

Trypanosoma brucei ornithine decarboxylase, expressed and purified from E. coli, has been crystallized by the vapor diffusion method using PEG 3350 as a precipitant. The crystals belong to the monoclinic space group P21 and have cell constants of a = 66.3 Å, b = 151.8 Å, c = 83.7 Å, and β = 101.2°. While larger crystals are twinned, smaller crystals (0.4 × 0.3 × 0.05 mm3) are single.
Philosophy, Self-Knowledge, and Personality in Iranian Teachers and Students of Philosophy

Like psychology, philosophy apparently operates from a commitment to the belief that self-knowledge should be a goal of disciplinary and personal development. Iranian teachers and students of philosophy responded to a Philosophical Orientations Scale created for this study that assessed the possible content of a high school philosophy course, along with instruments measuring self-knowledge, need for cognition, the five-factor model, anxiety, depression, and perceived stress. As the authors hypothesized, self-knowledge predicted higher levels of a philosophical orientation, even after controlling for the variance explained by need for cognition and openness to experience. Philosophical orientations and self-knowledge were also correlated with psychological adjustment, and teachers scored higher than students on these two sets of constructs. These data supported the hypothesis that personal and disciplinary interests in an adaptive self-knowledge converge in philosophy.
Simplifying the rounding for Newton-Raphson algorithm with parallel remainder

This work presents a variable latency rounding method based on the calculation in parallel of a remainder estimation for Newton-Raphson algorithm. The value obtained is the remainder of the algorithm result without any transformation. Because of this a new rounding method based on this value has to be proposed. This method avoid the traditional remainder calculation in 91% of the cases for division and 88% of the cases for square root.
R-factor, Free R, and Complete Cross-Validation for Dipolar Coupling Refinement of NMR Structures

NMR structure determination of macromolecules involves a minimization problem in which atomic models, subject to restraints relating to idealized covalent geometry and nonbonded contacts, are fitted to experimental observables. The latter comprise restraints between atoms separated by ≤6 A, such as NOE-derived interproton distances, torsion angles, coupling constants, and chemical shifts, as well as restraints that provide direct information on long-range order such as dipolar couplings. An expression for the dipolar coupling R-factor is derived which provides a quantitative and readily interpretable measure of the agreement between observed and calculated dipolar couplings. The dipolar R-factor expresses the ratio of the observed rms difference between observed and calculated values with that expected for a totally random distribution of vectors. The latter can be calculated exactly from the magnitude of the alignment tensor. The dipolar R-factor scales between 0 and 1, where a value of 0 indicates perfe.
Applying the INN model to the Maximum Clique problem

Max-Clique is the problem of finding the largest clique in a given graph. It is not only NP-hard, but, as recent results suggest, even hard to approximate. Nevertheless it is still very important to develop and test practical algorithms that will find approximate solutions for the maximum clique problem on various graphs stemming from numerous applications. Indeed, many different types of algorithmic approaches are applied to that problem. Several neural networks and related algorithms were applied recently to combinatorial optimization problems in general and to the Max-Clique problem in particular. These neural nets are dynamical system which minimize a cost (or computational ``energy``) function that represents the optimization problem, the Max-Clique in our case. Therefore they all belong to the class of integer programming algorithms surveyed in the Pardalos and Xue review. The work presented here is a development and improvement of a neural network algorithm that was introduced recently. In the previous work, we have considered two Hopfield type neural networks, the INN and the HcN, and their application to the max-clique problem. In this paper, I concentrate on the INN network and present an improved version of the t-A algorithm that was introduced in. The rest of thismore » paper is organized as follows: in section 2, I describe the INN model and how it implements a given graph. In section 3, it is characterized in terms of graph theory. In particular, the stable states of the network are mapped to the maximal cliques of its underling graph. In section 4, I present the t-Annealing algorithm and an improved version of it, the Adaptive t-Annealing. Several experiments done with these algorithms on benchmark graphs are reported in section 5, and the efficiency of the new algorithm is demonstrated. I conclude with a short discussion. « less
Speech Perception and Localization With Adults With Bilateral Sequential Cochlear Implants

This investigation reports measures of binaural hearing of all of our seven adults who have received sequential bilateral cochlear implants (range of time between implantation of 6 yr/8 mo and 17 yr). All subjects used both devices in everyday life. The internal array, number of channels, rate, and signal processing strategies were usually quite different between devices. Speech recognition was tested by using words in quiet and sentences in noise with the sentence stimuli presented from the front and the noise presented from the front, the right, or the left at a 90° angle. Bilateral localization was tested by using an everyday sounds test with stimuli presented from one of eight loudspeakers. Results showed that all subjects received a significant bilateral improvement on at least one speech perception test compared to either implant alone. Four of seven subjects with bilateral devices demonstrated some (root-mean-square error below 30°) localization abilities. The two subjects tested unilaterally before receiving a second implant showed a bilateral improvement on localization after implantation of the second side. We conclude that sequential implants can be beneficial even after many years of monaural use and even with very different cochlear implants.
Analysis of Allosteric Effector Binding Sites of Potato ADP-glucose Pyrophosphorylase through Reverse Genetics*

ADP-glucose pyrophosphorylase (AGPase) is a key regulatory enzyme of bacterial glycogen and plant starch synthesis as it controls carbon flux via its allosteric regulatory behavior. Unlike the bacterial enzyme that is composed of a single subunit type, the plant AGPase is a heterotetrameric enzyme (α2β2) with distinct roles for each subunit type. The large subunit (LS) is involved mainly in allosteric regulation through its interaction with the catalytic small subunit (SS). The LS modulates the catalytic activity of the SS by increasing the allosteric regulatory response of the hetero-oligomeric enzyme. To identify regions of the LS involved in binding of effector molecules, a reverse genetics approach was employed. A potato (Solanum tuberosum L.) AGPase LS down-regulatory mutant (E38A) was subjected to random mutagenesis using error-prone polymerase chain reaction and screened for the capacity to form an enzyme capable of restoring glycogen production in glgC−Escherichia coli. Dominant mutations were identified by their capacity to restore glycogen production when the LS containing only the second site mutations was co-expressed with the wild-type SS. Sequence analysis showed that most of the mutations were decidedly nonrandom and were clustered at conserved N- and C-terminal regions. Kinetic analysis of the dominant mutant enzymes indicated that theK m values for cofactor and substrates were comparable with the wild-type AGPase, whereas the affinities for activator and inhibitor were altered appreciably. These AGPase variants displayed increased resistance to Pi inhibition and/or greater sensitivity toward 3-phosphoglyceric acid activation. Further studies of Lys-197, Pro-261, and Lys-420, residues conserved in AGPase sequences, by site-directed mutagenesis suggested that the effectors 3-phosphoglyceric acid and Pi interact at two closely located binding sites.
The role of intraluminal radiotherapy and concurrent 5‐fluorouracil infusion in the management of carcinoma esophagus: A pilot study

Fifty patients with carcinoma of the esophagus were entered in a randomized pilot study to test the efficacy of intraluminal radiotherapy (ILRT) and concurrent 5‐fluorouracil (5‐FU) infusion. The median age was 65 years, with 80% having middle third lesions; in 62%, the lesions were longer than 5 cm. After external beam therapy of 50 Gy in 5 weeks, patients were randomized to receive chemotherapy. Significant improvement in dysphagia was recorded in 76% patients with complete response in 47 cases ranging from 6 to 27 months. The overall survival at 2 years was 15% with ILRT alone versus 22% with ILRT plus 5‐FU infusion.
Evaluating levels of PCR efficiency and genotyping error in DNA extracted from engorged and non‐engorged female Dermacentor variabilis ticks

Polymerase chain reaction (PCR)‐based methods are increasingly used to elucidate tick biology. However, DNA extracted from ticks may provide poor PCR templates as a result of PCR inhibition by mammalian blood or contamination by male DNA (in fertilized females). In this study, the effects of removing the bloodmeal and reproductive organs were evaluated through paired DNA extractions in engorged and non‐engorged Dermacentor variabilis (Say) (Acari: Ixodidae), prior to PCR amplification at 12 microsatellites. The first extraction utilized only mouthparts and legs (‘mouthpart’ samples) and the second utilized tick bodies (‘body’ samples). The results indicated that contamination by male DNA was an unlikely source of genotyping error in mouthpart and body samples. Engorged females showed higher levels of PCR inhibition in body vs. mouthpart samples, with a 29% decrease in amplification success rates per PCR and a 10‐fold increase in levels of missing genotypes in body samples. By contrast, non‐engorged females showed little difference in amplification success rates or numbers of missing genotypes in body vs. mouthpart samples. We discuss analytical concerns related to this systematic bias in PCR problems and recommend the removal of the bloodmeal and reproductive organs prior to DNA extraction, especially in engorged female ticks.
Quantum-Gravitational Effects on Primordial Power Spectra in Slow-Roll Inflationary Models

We review the computation of the power spectra of inflationary gauge-invariant perturbations in the context of canonical quantum gravity for generic slow-roll models. A semiclassical approximation, based on an expansion in inverse powers of the Planck mass, is applied to the complete Wheeler–DeWitt equation describing a perturbed inflationary universe. This expansion leads to a hierarchy of equations at consecutive orders of the approximation and allows us to write down a corrected Schrodinger equation that encodes information about quantum-gravitational effects. The analytical dependence of the correction to the power spectrum on the wavenumber is obtained. Nonetheless, some numerical work is needed in order to obtain its precise value. Finally, it is shown that the correction turns out to be positive, which leads to an enhancement of the power spectrum especially prominent for large scales. We will also discuss whether this correction leads to a measurable effect in the cosmic microwave background anisotropies.
HEMATOPOIESIS AND STEM CELLS Adult hematopoietic stem cells lacking Hif-1 a self-renew normally

MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, United Kingdom; Klinik fuer Haematologie, Onkologie und Stammzelltransplantation, Universitaetsklinikum Aachen, Aachen, Germany; Paul O’Gorman Leukaemia Research Centre, Institute for Cancer Sciences, University of Glasgow, Glasgow, United Kingdom; and Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
S 2 : The algebra of flexible cost functions Supporting information for HIV Treatment as Prevention : Modelling the Cost of Antiretroviral Treatment-State of the Art and Future Directions

A “cost function” is a mathematical function that defines the relationship between an output produced, here defined as patient-years (or -months) of antiretroviral therapy (ART), and the cost of the resources consumed in that production. A cost function, either explicit or implicit, is a necessary component of any estimate of the costs and benefits of ART service delivery. This appendix gives supporting details on the mathematical distinction between two classes of cost functions, which we refer to as “accounting identity” cost functions and “flexible” cost functions. Our purpose is not to elevate one of these types of cost functions over the other in all situations, but to distinguish them as distinct approaches to projecting costs, each of which has its strengths and weaknesses. In modelling practice, the most useful cost function might be one or the other or, in some cases, a hybrid of the two.
Analysing high frame-rate camera tracking

High frame-rate offers benefits of robust and accurate camera tracking for rapid motion. However, the benefits are generally understated arguing that it is not possible to operate on high frame-rates due to stringent processing budgets and that even today 1060Hz is treated as a standard real-time frame-rate range. How exactly does the choice of a given frame-rate varies as computational budget is changed? This thesis explores the possibilities of tracking at frame-rates higher than this range and argues that the computational cost per frame in trackers that use prediction is substantially reduced when the frame-rate is increased. Additionally, considering the physics of image formation, high frame-rate implies that the upper bound on the shutter time is reduced leading to less motion blur but more noise. On the other hand, low frame-rate often leads to motion blur but reduced noise in the images. Carefully considering the scene lighting that affects the image noise and the camera motion that affects the motion blur and putting these factors together, how are application-dependent performance requirements of accuracy, robustness and computational cost optimised as frame-rate varies? We study 3D camera tracking from a known rigid model as our test problem and analyse the fundamental image alignment approach to understand the choice of frame-rate that affects tracking. We systematically investigate this via a careful synthesis of photorealistic video using ray-tracing of detailed 3D scene, experimentally obtained photo-realistic reponse and noise models and rapid camera motions and later validate the conclusions with a well-controlled real experiment. The thesis provides quantitative conclusions about frame-rate selection, fundamental connections between frame-rate and image resolution and highlights the crucial role of full consideration of physical image formation process in pushing tracking performance.
SPCA: a no-reference image quality assessment based on the statistic property of the PCA on nature images

Despite the acceptable performance of current full-reference image quality assessment (IQA) algorithms, the need for a reference signal limits their application, and calls for reliable no-reference algorithms. Most no-reference IQA approaches are distortion specific, aiming to measure image blur, JPEG blocking or JPEG2000 ringing artifacts respectively. In this paper, we proposed a no-reference IQA algorithm based on the statistic property of principal component analysis on nature image, named SPCA, which does not assume any specific type of distortion of the image. The method gets statistics of discrete cosine transform coefficients from the distort image’s principal components. Those features are trained by 􀟥-support vector regression method and finally test on LIVE database. The experimental results show a high correlation with human perception of quality (averagely over 90% by scores of SROCC), which is fairly competitive with the existing no-reference IQA metrics.
[Spanish adaptation of the disease-specific questionnaire MSQOL-54 in multiple sclerosis patients].

INTRODUCTION The Multiple Sclerosis Quality of Life 54 (MSQOL-54) is a health-related quality of life specific questionnaire for multiple sclerosis (MS) patients. The objective of this study was to develop the Spanish version of the MSQOL-54 and to obtain a conceptually equivalent version to the original one for its use in patients with MS in the first phase of the project. METHODS A transcultural adaptation procedure was designed according to the following phases: a) two independent translations made by bilingual native Spanish speaking translators (forward translation); b) a revision of the items by an expert panel; c) a back translation by a bilingual native English speaking person; d) comparison with the original version (expert panel and advise by the original authors), and e) cognitive debriefing (interviews with subjects with MS) to test the comprehension and feasibility of the instrument. RESULTS Ten interviews were carried out with 5 men and 5 women with MS, aged 21 to 54 years, with different education levels and EDSS scores ranging from 1,0 to 8,0. Most of the patients found the questionnaire easy to fill out and the understanding favorable. Only one item (item 51) was modified after the cognitive debriefing to improve its comprehension. Finally, a final pretest version was obtained. CONCLUSIONS The procedure carried out maximizes the conceptual equivalence between the original MSQOL-54 and the translated version and shows that the Spanish pre-test version is comprehensible and its administration feasible in patients with MS. The psychometric properties must be evaluated in the next phase of the project.
Sensitive kinetic bioluminescent assay of glycerol release from human fat cells.

A sensitive and accurate assay of lipolysis has been developed, measuring the rate of glycerol release from fat cells with a bioluminescent assay. The rate of glycerol-dependent ATP-consumption in a system consisting of glycerokinase, ATP, luciferin, and luciferase was determined kinetically as a decrease of the ATP-induced luminescence and used for calculation of the concentration of glycerol. Under the conditions employed, it was possible to measure the concentration of glycerol down to a level of about 0.5 micron mol/l. Under the same conditions, the detection limit of the usual fluorometric method was about 15 micron mol/l. The coefficient of variation obtained with the bioluminescent assay was 11% at a level of 1.0 micron mol of glycerol, 2-6% at a level of about 5 micron mol/l, and 1-3% at a level of about 20 micron mol/l. Satisfactory results were obtained in different recovery experiments. Using human fat cells, it was possible to determine the rate of glycerol release with a cell concentration in the medium of only 5,000-10,000 cells/ml. It is concluded that the bioluminescent assay of glycerol release should be preferred when there is a demand for sensitivity, e.g., when the rate of lipolysis is low and when only a small amount of biopsy material is available.
Creation of sub-diffraction optical needle by nonlinear super-oscillatory lens

We demonstrate a novel nonlinear optical super-oscillatory lens, i.e. a periodically poled LiTaO<sub>3</sub> nonlinear photonic crystal, to create an optical needle with a sub-diffraction beam size of 0. 43λ<sub>SH</sub> and an ultra-long length of 40λ<sub>SH</sub>.
Insomnia Management in the Australian Primary Care Setting

ABSTRACT Background and Objective: Insomnia is one of the most prevalent and costly sleep disorders presenting in general practice, and when left untreated, has major health consequences. However, studies are limited on how general practitioners respond to this health issue, especially since the reconceptualization of insomnia in DSM 5. Therefore, the aim of this study was to explore how insomnia is diagnosed and treated in Australian general practices. Participants: Twenty-four (54% male) general practitioners were recruited throughout the greater Sydney metropolitan area in New South Wales using the professional network of research team members and snowballing technique. Methods: Participants were interviewed using a semi-structured interview guide. The audio-taped interviews were transcribed verbatim and a framework approach was used for analysis of transcribed data. Results: Participant’s responses highlighted that despite being a frequent presentation, insomnia is often trivialized with a low recognition rate in general practices. Lack of support and clear and effective management guidelines for general practitioners are the perceived barriers to early recognition of insomnia in general practices. Treating the underlying causes and initiating the treatment with general practitioners to manage insomnia. Medications including off-label antidepressants are often prescribed based on perceived patient expectation for a prescription. Conclusion: Findings of this exploratory study suggest the need for clearly contextualized guidelines that include information about a patient’s insomnia experience and treatment expectations. Another significant implication of this study is the need to develop and evaluate a model of collaborative sleep health services in general practice.
Factors affecting colonization and dissemination of Candida albicans from the gastrointestinal tract of mice

Male ICR Swiss mice (2 to 3 months old) were fed Candida albicans in their drinking water for 3 days, followed by no treatment, antibiotics in their drinking water (daily), or immunosuppressants given by intraperitoneal injection (two to three times weekly) over a 3- to 4-week period. The organs of animals were processed to determine the numbers of C. albicans and total aerobic bacteria per g of tissue. Untreated animals had mean Candida counts during the 1-month period of 10(2.3) CFU/g of cecum. Animals in six of eight antibiotic-treated groups had mean cecal Candida counts higher than those of control animals (P less than 0.05), with clindamycin-gentamicin producing the highest counts (10(4.7) CFU/g). Cyclophosphamide produced counts (10(4.3) CFU/g) which were higher (P less than 0.05) than those resulting from methotrexate (10(3.0) CFU/g) or steroid (10(2.7) CFU/g) treatment. Cyclophosphamide-clindamycin-gentamicin treatment was associated with the highest (P less than 0.05) levels of Candida colonization (10(6.5) CFU/g). Mice receiving immunosuppressants plus clindamycin-gentamicin were more likely to disseminate C. albicans than were mice receiving antibiotics alone (P less than 0.001). Our findings suggest that colonization of the guts of mice by C. albicans can be facilitated by manipulating the aerobic, anaerobic, or both types of gut flora. The combined effect of immunosuppressants on both Candida gut colonization and dissemination appears multifactorial and deserves further investigation.