Miracle-dz/UniFAR-FTUs huggingface dataset:
Edinburgh Research Explorer Identification and stage-specific association with the translational apparatus of TbZFP3, a CCCH protein that promotes trypanosome life-cycle development

The post-transcriptional control of gene expression is becoming increasingly important in the understanding of regulated events in eukaryotic cells. The parasitic kinetoplastids have a unique reliance on such processes, because their genome is organized into polycistronic transcription units in which adjacent genes are not coordinately regulated. Indeed, the number of RNA-binding proteins predicted to be encoded in the genome of kinetoplastids is unusually large, invoking the presence of unique RNA regulators dedicated to gene expression in these evolutionarily ancient organisms. Here, we report that a small CCCH zinc finger protein, TbZFP3, enhances development between life-cycle stages in Trypanosoma brucei. Moreover, we demonstrate that this protein interacts both with the translational machinery and with other small CCCH proteins previously implicated in trypanosome developmental control. Antibodies to this protein also co-immunoprecipitate EP procyclin mRNA and encode the major surface antigen of insect forms of T. brucei. Strikingly, although TbZFP3 is constitutively expressed, it exhibits developmentally regulated association with polyribosomes, and mutational analysis demonstrates that this association is essential for the expression of phenotype. TbZFP3 is therefore a novel regulator of developmental events in kinetoplastids that acts at the level of the post-transcriptional control of gene expression.
A new approximation of the Schur complement in preconditioners for PDE‐constrained optimization

Saddle point systems arise widely in optimization problems with constraints. The utility of Schur complement approximation is now broadly appreciated in the context of solving such saddle point systems by iteration. In this short manuscript, we present a new Schur complement approximation for PDE‐constrained optimization, an important class of these problems. Block diagonal and block triangular preconditioners have previously been designed to be used to solve such problems along with MINRES and non‐standard Conjugate Gradients, respectively; with appropriate approximation blocks, these can be optimal in the sense that the time required for solution scales linearly with the problem size, however small the mesh size we use. In this paper, we extend this work to designing such preconditioners for which this optimality property holds independently of both the mesh size and the Tikhonov regularization parameter β that is used. This also leads to an effective symmetric indefinite preconditioner that exhibits mesh and β independence. We motivate the choice of these preconditioners based on observations about approximating the Schur complement obtained from the matrix system, derive eigenvalue bounds that verify the effectiveness of the approximation and present numerical results that show that these new preconditioners work well in practice. Copyright © 2011 John Wiley & Sons, Ltd.
Optofluidic Microlasers based on Femtosecond Micromachining Technology

Abstract We present the different optofluidic lasers which have been realized using the Femtosecond Micromachining technique to fabricate the monolithic optofluidic structures in glass chips. We show how the great flexibility of this 3D technique allows getting different kind of optical cavities. The most recent devices fabricated by this technique as ring shaped and Fabry-Perot resonators show excellent emission performances.We also point out how the addition of the inkjet printing technique provides further opportunities in realizing optofluidic chips.
Dual Neonate Vaccine Platform against HIV-1 and M. tuberculosis

Acquired immunodeficiency syndrome and tuberculosis (TB) are two of the world's most devastating diseases. The first vaccine the majority of infants born in Africa receive is Mycobacterium bovis bacillus Calmette-Guérin (BCG) as a prevention against TB. BCG protects against disseminated disease in the first 10 years of life, but provides a variable protection against pulmonary TB and enhancing boost delivered by recombinant modified vaccinia virus Ankara (rMVA) expressing antigen 85A (Ag85A) of M. tuberculosis is currently in phase IIb evaluation in African neonates. If the newborn's mother is positive for human immunodeficiency virus type 1 (HIV-1), the baby is at high risk of acquiring HIV-1 through breastfeeding. We suggested that a vaccination consisting of recombinant BCG expressing HIV-1 immunogen administered at birth followed by a boost with rMVA sharing the same immunogen could serve as a strategy for prevention of mother-to-child transmission of HIV-1 and rMVA expressing an African HIV-1-derived immunogen HIVA is currently in phase I trials in African neonates. Here, we aim to develop a dual neonate vaccine platform against HIV-1 and TB consisting of BCG.HIVA administered at birth followed by a boost with MVA.HIVA. 85A. Thus, mMVA.HIVA. 85A and sMVA.HIVA. 85A vaccines were constructed, in which the transgene transcription is driven by either modified H5 or short synthetic promoters, respectively, and tested for immunogenicity alone and in combination with BCG.HIVA222. mMVA.HIVA. 85A was produced markerless and thus suitable for clinical manufacture. While sMVA.HIVA. 85A expressed higher levels of the immunogens, it was less immunogenic than mMVA.HIVA. 85A in BALB/c mice. A BCG.HIVA222–mMVA.HIVA. 85A prime-boost regimen induced robust T cell responses to both HIV-1 and M. tuberculosis. Therefore, proof-of-principle for a dual anti-HIV-1/M. tuberculosis infant vaccine platform is established. Induction of immune responses against these pathogens soon after birth is highly desirable and may provide a basis for lifetime protection maintained by boosts later in life.
Homomorphic Encryption and the BGN Cryptosystem

• Gen(): Choose an elliptic curve E/Fp with a point P of prime order n, and an integer s R ← [1, n]. Output pk = (P,Q = [s]P ) and sk = s. • Enc(pk,M): Let pk = (P,Q) and interpret M as a point on E(Fp). Choose r R ← [1, n] and output C = ([r]P,M + [r]Q). • Dec(C, sk). Let sk = s and C = (C1, C2). Output M ′ = C2 − [s]C1. Suppose we have two messagesM,M ′ ∈ E(Fp) and we compute the encryptions C = Enc(pk,M) = ([r]P,M + [r]Q) and C ′ = Enc(pk,M ′) = ([r′]P,M ′ + [r′]Q). Then C +C ′ (added componentwise) is equal to ([r + r′]P, (M + M ′) + [r + r′]Q) — so this is an encryption of M + M ′. Thus given two encryptions of messages, we can obtain an encryption of the sum of the messages without decrypting. (Indeed, the system remains semantically secure.) We say the system is “homomorphic”: encryption computes a group homomorphism from the message space to the ciphertext space. When M and M ′ are points on an elliptic curve, adding the two messages might not make much sense in terms of the underlying meaning of the messages. It would be better if M and M ′ were integers. For example, if M and M ′ represent salaries of Stanford professors, then adding them gives the sum of the salaries (and subsequently dividing by 2 gives the average). So here’s a variant of ElGamal that encrypts integers:
Comparative analysis of the effect of silver nanoparticle and silver nitrate on morphological and anatomical parameters of banana under in vitro conditions

ABSTRACT Toxicological studies of manufactured nanomaterials are getting increasingly significant due to their continuous environmental release through various commercial products. Thus in the study, banana variety Grandnaine was cultured in rooting media with various concentrations of AgNPs and AgNO3 for studying its effect on shoot length, root length, length and width of the longest leaf, fresh weight and dry weight. Interestingly, all the morphological parameters analyzed were found not to have any significant variation under various treatments made. The anatomy of the roots of plants under different treatments showed slight increase in the number of metaxylem elements at higher concentrations of AgNO3 compared to control. But the effect of AgNPs on number of metaxylem elements was at par with that of the control. The lack of toxicity of AgNP on banana tissue cultured plants as confirmed in the study offers opportunities to explore the development of NP based formulations for the enhancement of productivity of economically important plants like banana.
Surgical Site Infections and Other Postoperative Complications following Prophylactic Anticoagulation in Total Joint Arthroplasty

Background Anticoagulants reduce the risk of venous thromboembolism (VTE) after total joint replacement. However, concern remains that pharmacologic VTE prophylaxis can lead to bleeding, which may impact on postoperative complications such as infections and reoperations. Methods and Findings From the Global Orthopedic Registry (GLORY), we reviewed 3,755 patients in US who elected for primary total hip or knee arthroplasty, received either warfarin or low molecular weight heparin (LMWH) as VTE prophylactics, and had up-to-90-day follow-up after discharge. We compared incidence rates of VTE, infections and other complications between LMWH and warfarin groups, and used multivariate analyses with propensity score weighting to generate the odds ratio (OR). Patients receiving LMWH tended to be older and higher in the American Society of Anesthesiologists grade scores. In contrast, warfarin was used more frequently for hip arthroplasty with longer duration among patients with more pre-existing comorbidity (all P<0.02). A weight variable was created with propensity score to account for differences in covariate distributions. Propensity score-weighted analyses showed no differences in VTE complications. However, compared to warfarin, LMWH was associated with significantly higher rates of bleeding (6.2% vs. 2.1%; OR = 3.82, 95% confidence interval [CI], 2.64 to 5.52), blood transfusion (29.4% vs. 22.0%; OR = 1.75, 95% CI, 1.51 to 2.04), reoperations (2.4% vs. 1.3%; OR = 1.77, 95% CI, 1.07 to 2.93) and infections (1.6% vs. 0.6%; OR = 2.79, 95% CI, 1.42 to 5.45). Similar results were obtained from compliant uses of warfarin (26%) and LMWH (62%) according to clinical guidelines. While surgical site infections were mostly superficial, current study was underpowered to compare incidence rates of deep infections (<1.0%). Conclusions Surgical site infections and reoperations in 3 months following primary total joint arthroplasty may be associated with anticoagulant use that exhibited higher bleeding risk. Long-term complications and deep wound infections remain to be studied.
Tower Controllers ’ Assessment of the Spot and Runway Departure Advisor ( SARDA ) Concept

Airports are often a capacity-limiting constraint for the rest of the National Airspace System (NAS). A recent effort investigated methods to improve surface operations by supplying optimized scheduling and sequencing advisories for the Ground and Local controllers working at Air Traffic Control Towers. The tool is collectively known as the Spot and Runway Departure Advisor (SARDA). A series of high fidelity human-in-the-loop simulations was conducted to assess scheduling performance and their effects on the human operators. This paper documents the impact of the advisories on controllers’ workload, situation awareness (SA), and usability. Fifty-six high fidelity human-inthe-loop simulations were conducted using a matrix of traffic level (normal and high) and advisory display formats (data tag and timeline). Results revealed that the high traffic level increased perceived workload for both Ground and Local controllers. Local and Ground controllers also reported a decrease in subjective SA in the high traffic condition. There was no significant effect of traffic level or advisory usage on the objective SA measure, although their interaction was statistically significant. For Ground, objective SA decreased in the high traffic but not during the normal traffic level. Ground controllers showed a preference for using the timeline format by reducing scans for information and aiding with future planning. Feedback also revealed that future work should focus on harmonization between the optimization model and the human planning model, thus providing a transparent planning and execution strategy. Keywords-component; surface scheduler; optimizer; airport simulator; human factors; workload; situation awareness; usability
Greek Wordnet Extension in the Domain of Psychology and Computer Science

In this paper we present the investigative construction-methodology of a Greek dictionary in the domain of psychology (PsyGrTerms) and in the domain of computer science (CompScieTerms). We also present the construction methodology of PsychoGreekWordnet (PsyGrWn), a semantic Greek lexicon in the domain of psychology, stored in XML format. It contains synonym-sets of some of the most important Greek terms of contemporary psychology and their lexical semantic relations (Hypernymy, Holonymy), without recursive (cyclic) definitions or ambiguous definitions. Then we compare the searching results a) between English WordNet 2.0. c, Greek Wordnet 0.9. a and PsyGrWn, and b) between English WordNet 2.0. c, Greek Wordnet 0.9. a and CompScieTerms. Problematic issues and practical solutions adopted or proposed are described. Finally we discuss the foreseen advantages and improvements.
Semi-preemptible locks for a distributed file system

Many applications require the ability to obtain exclusive access to data, where an application is granted privileges to an object that cannot be preempted and limits the actions of other processes. Local file systems support exclusive access to files by maintaining information about the access rights of current open file instances, and checking subsequent opens for compatibility. Implementing exclusive access in this manner for distributed file systems degrades performance by requiring every open file to be registered with a server that maintains global open state. We introduce a distributed lock for managing file access, called a semi-preemptible lock, that avoids this performance limitation. Clients locally grant open requests for files that are consistent with a distributed semipreemptible lock that they hold. File system clients retain or cache distributed locks, even in the absence of open file instances. When a file access lock is already cached, a client services open requests. Without a server message, improving performance by exploiting locality, the affinity of files to clients.
1H NMR characterisation of pore water in cement materials

This paper presents summary results of a Round Robin Trial to examine the reproducibility and robustness of 1H NMR relaxation analysis of water in cements. The results have elsewhere been used to evidence a good practice guide for the characterization of cement using 1H NMR relaxation analysis. A summary of the good practice is presented
A dynamic branch and bound approach for robotic rescheduling with randomly arriving jobs

This paper addresses a rescheduling problem in a robotic cell where a material handling robot is responsible to transport parts from one workstation to another and the different jobs (parts) arrive at the cell randomly. Our objective is to minimize the total completion time of all the jobs by dynamically changing the current schedule. Following a robotic rescheduling framework to find a new schedule, the problem is reduced to resolving a local deterministic robotic scheduling problem to minimize the total completion time. After that the local problem is formulated, according to the processing recipes of the jobs and the state of the robotic cell. We propose a branch and bound algorithm with a dynamic enumeration mechanism to solve the localized problem. Our proposed algorithm is evaluated by a numerical example.
Effects of Nitroglycerin on “Maximal’ Oxygen Intake and Exercise Electrocardiogram in Coronary Heart Disease

Oxygen intake (VO2) was measured during the last few minutes of a multistage treadmill test of maximal exercise in 12 healthy middle-aged persons, 32 patients with angina, and 23 survivors of myocardial infarction free of angina. Repetition of the same test, after each individual rested 30 min and took 0.4 mg nitroglycerin sublingually, increased VO2 max in patients with angina (by 14.5%, P < 0.001) and in patients with prior infarction (by 6%, P < 0.005) but not in healthy persons. Angina at VO2 max was prevented in 12 patients. Maximal heart rate was increased by 11% in the angina group and by 4% in the myocardial infarction group; the maximal blood pressure-heart rate product was increased (P < 0.005) only in patients with angina. [See Equation in PDF file] voltages from 50 to 69 msec after the nadir of S wave (S-TB) were quantified by computer averaging of 100 beat samples at several intervals during and after exercise. The amount of [See Equation in PDF file] depression during and after exercise was significantly reduced after administration of nitroglycerin in all three groups.We conclude that nitroglycerin: (1) increases maximal circulatory conductance of O2 in patients with coronary heart disease, whether or not limited by angina, mainly by increased maximal heart rate, and (2) lessens evidence of electrocardiographic myocardial ischemia and lowers frequency if angina pectoris despite the same or a higher pressure-rate index. These effects suggest a reduction in peripheral vascular tone and left ventricular end-diastolic pressure and volume with nitroglycerin.
Robust adaptive beamforming using worst-case performance optimization: a solution to the signal mismatch problem

Adaptive beamforming methods are known to degrade if some of underlying assumptions on the environment, sources, or sensor array become violated. In particular, if the desired signal is present in training snapshots, the adaptive array performance may be quite sensitive even to slight mismatches between the presumed and actual signal steering vectors (spatial signatures). Such mismatches can occur as a result of environmental nonstationarities, look direction errors, imperfect array calibration, distorted antenna shape, as well as distortions caused by medium inhomogeneities, near-far mismatch, source spreading, and local scattering. The similar type of performance degradation can occur when the signal steering vector is known exactly but the training sample size is small. In this paper, we develop a new approach to robust adaptive beamforming in the presence of an arbitrary unknown signal steering vector mismatch. Our approach is based on the optimization of worst-case performance. It turns out that the natural formulation of this adaptive beamforming problem involves minimization of a quadratic function subject to infinitely many nonconvex quadratic constraints. We show that this (originally intractable) problem can be reformulated in a convex form as the so-called second-order cone (SOC) program and solved efficiently (in polynomial time) using the well-established interior point method. It is also shown that the proposed technique can be interpreted in terms of diagonal loading where the optimal value of the diagonal loading factor is computed based on the known level of uncertainty of the signal steering vector. Computer simulations with several frequently encountered types of signal steering vector mismatches show better performance of our robust beamformer as compared with existing adaptive beamforming algorithms.
Performance and Portability with OpenCL for Throughput-Oriented HPC Workloads across Accelerators, Coprocessors, and Multicore Processors

Ever since accelerators and coprocessors became the mainstream hardware for throughput-oriented HPC workloads, various programming techniques have been proposed to increase productivity in terms of both the performance and ease-of-use. We evaluate these aspects of OpenCL on a number of hardware platforms for an important subset of dense linear algebra operations that are relevant to a wide range of scientific applications. Our findings indicate that OpenCL portability has improved since our previous publication and many new and surprising usage scenarios are possible that rival those available after decades of software development on the CPUs. The combined performance-portability metric, even though not promised by the OpenCL standard, reflects the need for tuning performance-critical operations during the porting process and we show how a large portion of the available efficiency is lost if the tuning is not done correctly.
Generative Encoder-Decoder Models for Task-Oriented Spoken Dialog Systems with Chatting Capability

Generative encoder-decoder models offer great promise in developing domain-general dialog systems. However, they have mainly been applied to open-domain conversations. This paper presents a practical and novel framework for building task-oriented dialog systems based on encoder-decoder models. This framework enables encoder-decoder models to accomplish slot-value independent decision-making and interact with external databases. Moreover, this paper shows the flexibility of the proposed method by interleaving chatting capability with a slot-filling system for better out-of-domain recovery. The models were trained on both real-user data from a bus information system and human-human chat data. Results show that the proposed framework achieves good performance in both offline evaluation metrics and in task success rate with human users.
The ZVS-PWM active-clamping CUK converter

A CUK converter featuring clamping action, pulsewidth modulation, and soft-switching commutation is proposed to overcome the limitations of the conventional CUK converter. As the resonant circuits absorb almost all parasitic reactances of switches, including transistor output capacitances, this converter is suitable for high-frequency operation. Principle of operation, theoretical analysis, and simulation results are presented in this paper. Experimental results, taken from a laboratory prototype rated at 400 W, input voltage of 150 V, output voltage of 200 V, and operating at 100 kHz, are also presented. The efficiency obtained at full load of the power stage was 93%.
Review article: Geometric processing of remote sensing images: models, algorithms and methods

The geometric processing of remote sensing images becomes a key issue in multi-source data integration, management and analysis for many geomatic applications. This paper first reviews the source of geometric distortions, compares the different mathematical models being currently used for geometric distortion modelling, details the algorithms, methods and processing steps and finally tracks the error propagation from the input to the final output data.