Miracle-dz/UniFAR-FTUs huggingface dataset:
Introduction of a Synthetic CO2-fixing Photorespiratory Bypass into a Cyanobacterium

Background: Photorespiration limits carbon fixation. Results: Heterologous expression and functional activity of six enzymes from the 3-hydroxypropionate bi-cycle are demonstrated in cyanobacteria. Conclusion: A synthetic CO2-fixing photorespiratory bypass can be introduced into cyanobacteria. Significance: The results lay the foundation for expressing an alternative CO2 fixation pathway in cyanobacteria, algae, and plants. Global photosynthetic productivity is limited by the enzymatic assimilation of CO2 into organic carbon compounds. Ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO), the carboxylating enzyme of the Calvin-Benson cycle, poorly discriminates between CO2 and O2, leading to photorespiration and the loss of fixed carbon and nitrogen. With the advent of synthetic biology, it is now feasible to design, synthesize, and introduce biochemical pathways in vivo. We engineered a synthetic photorespiratory bypass based on the 3-hydroxypropionate bi-cycle into the model cyanobacterium, Synechococcus elongatus sp. PCC 7942. The heterologously expressed cycle is designed to function as both a photorespiratory bypass and an additional CO2-fixing pathway, supplementing the Calvin-Benson cycle. We demonstrate the function of all six introduced enzymes and identify bottlenecks to be targeted in subsequent bioengineering. These results have implications for efforts to improve photosynthesis and for the “green” production of high value products of biotechnological interest.
Sensitive multistep clinical molecular screening of 180 unrelated individuals with retinoblastoma detects 36 novel mutations in the RB1 gene

Retinoblastoma (RB) is a neoplasm of retinal origin caused by mutations in RB1, the retinoblastoma tumor suppressor gene. To facilitate genetics counseling and patient management, we adopted a multistep molecular screening assay for detecting RB1 mutations. This assay included DNA sequencing to identify mutations within coding exons and immediate flanking intronic regions, Southern blot analysis to characterize genomic rearrangements, and transcript analysis to characterize potential splicing mutations buried within introns. In a pilot investigation of 180 patients from North America, we identified germline RB1 mutations in 77 out of 85 bilateral RB patients (91%), 7 out of 10 familial unilateral (70%), and 6 out of 85 unilateral patients with no family history of RB (7%). Mutations included 36 novel alterations spanning the entire RB1 gene. Seven of these novel changes were missense or silent mutations. Sequence analysis predicted that, in five out of seven cases, the changes can cause aberrant splicing. This was confirmed by transcript analysis in four out of five cases. In addition, four intronic point mutations within nonconsensus sites activated cryptic splice sites. Without the transcript analysis, the significance of these 11 mutations would have remained undefined. In a separate investigation of a subset of unilateral RB tumors, we identified somatic biallelic RB1 gene inactivation in 34 out of 56 cases (61%) cases. In 14 tumors, only one of the two RB1 mutations could be detected, and in eight tumors, no mutations were detected. The absence of detectable RB1 mutations in eight bilateral cases and eight unilateral tumors suggests that alternative genetic mechanisms may underlie the development of RB in certain individuals. Hum Mutat 25:566–574, 2005. © 2005 Wiley‐Liss, Inc.
Breakdown of Solid Dielectrics in Divergent Fields

Breakdown channels are shown to propagate from steel needle-point electrodes embedded in polythene and polyisobutylene when the maximum effective stress at the end of the point reaches the intrinsic electric strength of the material at the test temperature. The average breakdown stress shows no significant variation with the radius of curvature of the point (for radii of 1? 20 micron), but, at room temperature, about 25% greater stress is required with a negative than with a positive point. These results are explained by the effect of enhanced conductivity and space-charge accumulation increasing the effective point radius to some 25 microns for positive and about 45 microns for negative points. The effect of polarity decreases with increasing temperature and is negligible at 100°C. The decrease of the average stress required for breakdown with increasing electrode separation is explained, and the same concept is used to predict the variation of the industrial electric strength of materials with specimen thickness. Factors affecting the industrial electric strength of materials are discussed and illustrated by tests on polythene, polystyrene and cellulose acetate, using British Standard electrodes in air and in clean and contaminated transformer oil.
Inhibition of Collagen Synthesis With Prolyl 4-Hydroxylase Inhibitor Improves Left Ventricular Function and Alters the Pattern of Left Ventricular Dilatation After Myocardial Infarction

Background—Left ventricular (LV) remodeling after myocardial infarction (MI) is associated with fibrosis, dilatation, and dysfunction. We postulated that prevention of fibrosis after MI with a prolyl 4-hydroxylase inhibitor (P4HI) would preserve LV function and attenuate LV enlargement. Methods and Results—Adult female rats (200 to 250 g) had experimental MI and were then randomized to treatment with P4HI (MI-FG041, n=29) or vehicle (MI-control, n=29) 48 hours after MI for 4 weeks in 2 phases. Echocardiograms were performed weekly with a 15-MHz linear transducer, and at 4 weeks, collagen isoform determinations and in vivo hemodynamics were performed. At randomization, the infarct size and LV function and size were similar in MI-FG041 and MI-control but significantly different from shams (n=9). At week 4, the LV function in MI-FG041 was significantly better than in MI-controls (fractional shortening 21% versus 16%, P =0.01; fractional area change 30% versus 19%, P =0.002; ejection fraction 35% versus 23%, P =0.001). In the FG041 group, LV area in systole was less (P <0.05), the dP/dtmax after isoproterenol was higher (P <0.05), and types I and III collagen in noninfarcted LV were less than in MI-control. The hydroxyproline/proline ratio was increased by 64% in MI-control and reduced to the sham value in MI-FG041 rats. In the scar tissue, it was reduced by 24% in MI-FG041. Conclusions—This study demonstrates that prevention of interstitial fibrosis with a P4H inhibitor alters the pattern of LV enlargement and produces partial recovery of LV function after MI.
Efficient Collision and Self-Collision Detection for Humanoids Based on Sphere Trees Hierarchies

We present an algorithm for computing compact sphere tree hierarchies over general 3D polygonal meshes for the purpose of efficient collision detection and minimum distance computation. The sphere tree construction method we use optimizes the location of the sphere centers and radii at each level of the hierarchy to compactly contain the underlying geometry. We enhance the hierarchy construction so that it can be applied to both self-collision and obstacle collision detection for articulated robots. Finally, we introduce distance range bounds that are effective for minimizing the overall number of required distance computations. The result is a faster algorithm that performs particularly well on collections of multiple mesh objects
Practice-Oriented Controversies and Borrowed Epistemic Credibility In Current Evolutionary Biology: Phylogeography As A Case Study

Philosophical treatments of scientific controversies usually focus on theory, excluding important practice related aspects. However, scientists in conflict often appeal to extra-theoretical and extra-empirical elements. To understand better the role that non-empirical elements play in scientific controversies, we introduce the notion of borrowed epistemic credibility, illustrating our proposal with a recent controversy in a field of evolutionary biology known as phylogeography. Our analysis shows how scientific controversies that spring from disagreements about methodological issues potentially involve deeper debates regarding what constitutes good science, prompting the re-examination of more general issues, such as the nature of inference, rationality, and objectivity.
LOCSVMPSI: a web server for subcellular localization of eukaryotic proteins using SVM and profile of PSI-BLAST

Subcellular location of a protein is one of the key functional characters as proteins must be localized correctly at the subcellular level to have normal biological function. In this paper, a novel method named LOCSVMPSI has been introduced, which is based on the support vector machine (SVM) and the position-specific scoring matrix generated from profiles of PSI-BLAST. With a jackknife test on the RH2427 data set, LOCSVMPSI achieved a high overall prediction accuracy of 90.2%, which is higher than the prediction results by SubLoc and ESLpred on this data set. In addition, prediction performance of LOCSVMPSI was evaluated with 5-fold cross validation test on the PK7579 data set and the prediction results were consistently better than the previous method based on several SVMs using composition of both amino acids and amino acid pairs. Further test on the SWISSPROT new-unique data set showed that LOCSVMPSI also performed better than some widely used prediction methods, such as PSORTII, TargetP and LOCnet. All these results indicate that LOCSVMPSI is a powerful tool for the prediction of eukaryotic protein subcellular localization. An online web server (current version is 1.3) based on this method has been developed and is freely available to both academic and commercial users, which can be accessed by at .
Community-based cardiovascular Risk Factors Intervention Strategies (CORFIS) in managing hypertension: A pragmatic non-randomised controlled trial.

BACKGROUND Hypertension is the number one cardiovascular risk factor in Malaysia. This study aimed to evaluate the effectiveness of a Community-Based Cardiovascular Risk Factors Intervention Strategies (CORFIS) in the management of hypertension in primary care. METHODS This is a pragmatic, non-randomized controlled trial. Seventy general practitioners (GPs) were selected to provide either CORFIS (44 GPs) or conventional care (26 GPs) for 6 months. A total of 486 hypertensive patients were recruited; 309 were in the intervention and 177 in the control groups. Primary outcome was the proportion of hypertensive patients who achieved target blood pressure (BP) of <140/90mmHg (for those without diabetes mellitus) and <130/80mmHg (with diabetes mellitus). Secondary outcomes include change in the mean/median BP at 6-month as compared to baseline. RESULTS The proportion of hypertensive patients who achieved target BP at 6-month was significantly higher in the CORFIS arm (69.6%) as compared to the control arm (57.6%), P=0.008. Amongst those who had uncontrolled BP at baseline, the proportion who achieved target BP at 6-month was also significantly higher in the CORFIS arm (56.6%) as compared to the control arm (34.1%), p<0.001. There was no difference in the patients who had already achieved BP control at baseline. There were significant reductions in SBP in the CORFIS arm (median -9.0mmHg; -60 to 50) versus control (median -2mmHg; -50 to 48), p=0.003; as well as in DBP (CORFIS arm: median -6.0mmHg; ranged from -53 to 30 versus control arm: median 0.0mmHg; ranged from -42 to 30), p<0.001. CONCLUSIONS Patients who received CORFIS care demonstrated significant improvements in achieving target BP.
Placing and Recalling Virtual Items on the Skin

The human skin provides an ample, always-on surface for input to smart watches, mobile phones, and remote displays. Using touch on bare skin to issue commands, however, requires users to recall the location of items without direct visual feedback. We present an in-depth study in which participants placed 30 items on the hand and forearm and attempted to recall their locations. We found that participants used a variety of landmarks, personal associations, and semantic groupings in placing the items on the skin. Although participants most frequently used anatomical landmarks (e.g., fingers, joints, and nails), recall rates were higher for items placed on personal landmarks, including scars and tattoos. We further found that personal associations between items improved recall, and that participants often grouped important items in similar areas, such as family members on the nails. We conclude by discussing the implications of our findings for design of skin-based interfaces.
Adaptation of offline vertical selection predictions in the presence of user feedback

Web search results often integrate content from specialized corpora known as verticals. Given a query, one important aspect of aggregated search is the selection of relevant verticals from a set of candidate verticals. One drawback to previous approaches to vertical selection is that methods have not explicitly modeled user feedback. However, production search systems often record a variety of feedback information. In this paper, we present algorithms for vertical selection which adapt to user feedback. We evaluate algorithms using a novel simulator which models performance of a vertical selector situated in realistic query traffic.
Negotiated tutoring : an approach to interaction in intelligent tutoring systems

This thesis describes a general approach to tutorial interaction in Intelligent Tutoring Systems, called "Negotiated Tutoring". Some aspects of the approach have been implemented as a computer program in the 'KANT' (Kritical Argument Negotiated Tutoring) system. Negotiated Tutoring synthesises some recent trends in Intelligent Tutoring Systems research, including interaction symmetry, use of explicit negotiation in dialogue, multiple interaction styles, and an emphasis on cognitive and metacognitive skill acquisition in domains characterised by justified belief. This combination of features has not been previously incorporated into models for intelligent tutoring dialogues. Our approach depends on modelling the high-level decision-making processes and memory representations used by a participant in dialogue. Dialogue generation is controlled by reasoning mechanisms which operate on a 'dialogue state', consisting of conversants' beliefs, a set of possible dialogue moves, and a restricted representation of the recent utterances generated by both conversants. The representation for conversants' beliefs is based on Anderson's (1983) model for semantic memory, and includes a model for dialogue focus based on spreading activation. Decisions in dialogue are based on preconditions with respect to the dialogue state, higher level educational preferences which choose between relevant alternative dialogue moves, and negotiation mechanisms designed to ensure cooperativity. The domain model for KANT was based on a cognitive model for perception of musical structures in tonal melodies, which extends the theory of Lerdahl and Jackendoff (1983). Our model ('GRAF' - GRouping Analysis with Frames) addresses a number of problems with Lerdahl and Jackendoff's theory, notably in describing how a number of unconscious processes in music cognition interact, including elements of top-down and bottom-up processing. GRAF includes a parser for musical chord functions, a mechanism for performing musical reductions, low-level feature detectors and a frame-system (Minsky 1977) for musical phrase structures.
Negative correlation between protozoal and bacterial levels in rumen samples and its relation to the determination of dietary effects on the rumen microbial population

The bacterial protein content and protozoal protein content of unfractionated samples from the liquid-small particle phase of the rumen were determined on the basis of direct microscopic measurement of bacteria numbers and protozoa numbers and cell volumes. Standard values of 8.7 X 10(-11) mg of protein per bacterial cell and 5.9 X 10(-11) mg/micron 3 of protozoa cell volume, obtained from analysis of isolated cells, were used to convert the microscopic measurements to an estimate of the protein content of the rumen sample. When the correlation between bacterial and protozoal protein levels was examined within groups of animals, a highly significant negative correlation between these two parameters was found (P less than 0.001). The variation among animals for total (bacterial plus protozoal) microbial protein was smaller than the variation among animals for bacterial or protozoal protein alone. There was also a highly significant positive correlation (P less than 0.001) between protozoal protein level and total microbial protein level. The variation found among animals in total microbial protein level could be reduced by using a regression equation determined for bacterial versus protozoal protein to correct for the different population dynamics of the two groups.
Effect of water on viscoelastic properties of oriental lacquer film

We noticed the Urushi film, by which oriental lacquer wares are prepared. The effect of water on mechanical properties of oriental lacquer film was investigated in a tensile test and a stress relaxation test. These tests were conducted under the various degrees of humidity. Oriental lacquer film had a tendency to became brittle under dry condition and to toughen under wet conditions. On the other hand, the film becomes sticky and soft under high humidity or in water. The relaxation modulus for this film was determined under the various degrees of humidity. This behavior changed largely depending upon humidity. Master curves on the result of stress relaxation test were prepared by applying the rule of time–temperature superposition. The temperature dependence of shift factor on the various degrees of humidity could be represented by the Williams–Landel–Ferry equation by changing two parameters, C1 and C2. © 1998 John Wiley & Sons, Inc. J Appl Polym Sci 69: 315–321, 1998
A Personalized Ontology Model for Web Information Gathering

As a model for knowledge description and formalization, ontologies are widely used to represent user profiles in personalized web information gathering. However, when representing user profiles, many models have utilized only knowledge from either a global knowledge base or a user local information. In this paper, a personalized ontology model is proposed for knowledge representation and reasoning over user profiles. This model learns ontological user profiles from both a world knowledge base and user local instance repositories. The ontology model is evaluated by comparing it against benchmark models in web information gathering. The results show that this ontology model is successful.
Multi-antenna scheme for high capacity transmission in the digital audio broadcasting

In this paper, we apply multi-antenna scheme to DAB system for high-rate transmission. In the MIMO-DAB system with a number of transmitting and receiving antennas increases the transmission rate efficiently with low multiplication operations. For channel estimation in the MIMO-DAB system, we propose a new PRS structure and evaluate the channel estimation performance. The proposed PRS structure can estimate multi-channel information based on the semi-blind processing. The performance of proposed PRS is compared with that of conventional training sequence employing Tarokh's transmission matrix. And also we investigate the performance limitation due to the imperfect channel estimation in a MIMO-DAB receiver. It has been shown that the MIMO-DAB system with multi-antennas can achieve the high-rate transmission for multimedia broadcasting and the performance of MIMO-DAB system is impaired by imperfect channel information.
Adaptive compute-and-forward with lattice codes over algebraic integers

We consider the compute-and-forward relay network with limited feedback. A novel scheme called adaptive compute-and-forward is proposed to exploit the channel knowledge by working with the best ring of imaginary quadratic integers. This is enabled by generalizing Construction A lattices to other rings of imaginary quadratic integers which may not form principal ideal domains and by showing such construction can produce good lattices for coding in the sense of Poltyrev and for MSE quantization. Since there are channel coefficients (complex numbers) which are closer to elements of rings of imaginary quadratic integers other than Gaussian and Eisenstein integers, by always working with the best ring among them, we can obtain better performance than that provided by working over Gaussian or Eisenstein integers.
Design of Closely Packed Pattern Reconfigurable Antenna Array for MIMO Terminals

In this communication, a compact pattern reconfigurable dual-antenna array is designed at 2.65 GHz for multiple-input multiple-output (MIMO) terminal applications, such as laptops. Each antenna is composed of two layers, i.e., the monopole layer and the planar inverted-F antenna (PIFA) layer. By switching the p-i-n diodes on each layer, its radiation patterns can be varied between conical and boresight patterns. Two such identical antennas are placed side by side on a common ground plane for MIMO application, providing altogether four operating modes. The center-to-center separation between the antennas is 0.25 wavelength, to keep the overall array compact. To facilitate an isolation of above 17 dB over all the modes for this compact array, two decoupling techniques based on the decoupling slits and the shielding wall are effectively combined. The envelope correlation coefficients (ECCs) of the far-field patterns in the four modes are below 0.05 in free space, and below 0.1 for most cases in the indoor and outdoor scenarios. The only exception is the monopole-PIFA mode in the outdoor scenario, but the ECC is still below 0.3 for this case. The measured efficiencies of the antennas are between −1.7 (68%) and −0.7 dB (85%) for all the modes. Therefore, good diversity and MIMO performances are expected for the proposed design.