Miracle-dz/UniFAR-FTUs huggingface dataset:
A Heterologous Prime-Boost Vaccination Strategy Comprising the Francisella tularensis Live Vaccine Strain capB Mutant and Recombinant Attenuated Listeria monocytogenes Expressing F. tularensis IglC Induces Potent Protective Immunity in Mice against Virulent F. tularensis Aerosol Challenge

ABSTRACT Francisella tularensis, the causative agent of tularemia, is a category A bioterrorism agent. A vaccine that is safer and more effective than the currently available unlicensed F. tularensis live vaccine strain (LVS) is needed to protect against intentional release of aerosolized F. tularensis, the most dangerous type of exposure. In this study, we employed a heterologous prime-boost vaccination strategy comprising intradermally administered LVS ΔcapB (highly attenuated capB-deficient LVS mutant) as the primer vaccine and rLm/iglC (recombinant attenuated Listeria monocytogenes expressing the F. tularensis immunoprotective antigen IglC) as the booster vaccine. Boosting LVS ΔcapB-primed mice with rLm/iglC significantly enhanced T cell immunity; their splenic T cells secreted significantly more gamma interferon (IFN-γ) and had significantly more cytokine (IFN-γ and/or tumor necrosis factor [TNF] and/or interleukin-2 [IL-2])-producing CD4+ and CD8+ T cells upon in vitro IglC stimulation. Importantly, mice primed with LVS ΔcapB or rLVS ΔcapB/IglC, boosted with rLm/iglC, and subsequently challenged with 10 50% lethal doses (LD50) of aerosolized highly virulent F. tularensis Schu S4 had a significantly higher survival rate and mean survival time than mice immunized with only LVS ΔcapB (P < 0.0001); moreover, compared with mice immunized once with LVS, primed-boosted mice had a higher survival rate (75% versus 62.5%) and mean survival time during the first 21 days postchallenge (19 and 20 days for mice boosted after being primed with LVS ΔcapB and rLVS ΔcapB/IglC, respectively, versus 17 days for mice immunized with LVS) and maintained their weight significantly better (P < 0.01). Thus, the LVS ΔcapB-rLm/iglC prime-boost vaccination strategy holds substantial promise for a vaccine that is safer and at least as potent as LVS.
Factor XI in haemostasis and thrombosis: Past, present and future

Thromb Haemost 2007; 98: 84–89 The discipline of haemostasis and thrombosis has set an example, perhaps more than other disciplines of Medicine, in discoveries based on observations of the so called “experiments of nature”. During a relatively short time of 13 years (1947 – 1960), most coagulation factors were identified in patients who presented with a bleeding tendency and were worked up by rather simple laboratory assays.This era of discoveries was followed by the characterization of the biochemical reactions involved in blood coagulation, delineation of the sequence of reactions in the coagulation pathways and more recently by unraveling the molecular genetic aspects of the various coagulation components. The objective of this review is to describe some of the major developments in understanding the role of factor (F)XI in haemostasis and thrombosis that have occurred over more than 50 years of research, and to highlight recent evidence which suggests that FXI deficiency can have an antithrombotic effect.
FastTargetPred: a program enabling the fast prediction of putative protein targets for input chemical databases

SUMMARY Several web-based tools predict the putative targets of a small molecule query compound by similarity to molecules with known bioactivity data using molecular fingerprints. In numerous situations, it would however be valuable to be able to run such computations on a local computer. We present FastTargetPred, a new program for the prediction of protein targets for small molecule queries. Structural similarity computations rely on a large collection of confirmed protein-ligand activities extracted from the curated ChEMBL 25 database. The program allows to annotate an input chemical library of ∼100k compounds within a few hours on a simple personal computer. AVAILABILITY AND IMPLEMENTATION FastTargetPred is written in Python 3 (≥3.7) and C languages. Python code depends only on the Python Standard Library. The program can be run on Linux, MacOS and Windows operating systems. Pre-compiled versions are available at https://github.com/ludovicchaput/FastTargetPred. FastTargetPred is licensed under the GNU GPLv3. The program calls some scripts from the free chemistry toolkit MayaChemTools. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Cysteine-Rich Secretory Protein 2 Binds to Mitogen-Activated Protein Kinase Kinase Kinase 11 in Mouse Sperm1

Abstract Cysteine-rich secretory protein (CRISP) 2 (previously TPX1) is a testis-enriched member of the CRISP family, and has been localized to both the sperm acrosome and tail. Like all members of the mammalian CRISP family, its expression pattern is strongly suggestive of a role in male fertility, but functional support for this hypothesis remains limited. In order to determine the biochemical pathways within which CRISP2 is a component, the putative mature form of CRISP2 was used as bait in a yeast two-hybrid screen of a mouse testis expression library. One of the most frequently identified interacting partners was mitogen-activated protein kinase kinase kinase 11 (MAP3K11). Sequencing and deletion experiments showed that the carboxyl-most 20 amino acids of MAP3K11 interacted with the CRISP domain of CRISP2. This interaction was confirmed using pull-down experiments and the cellular context was supported by the localization of CRISP2 and MAP3K11 to the acrosome of the developing spermatids and epididymal spermatozoa. Interestingly, mouse epididymal sperm contained an ∼60-kDa variant of MAP3K11, which may have been a result of proteolytic cleavage of the longer 93-kDa form seen in many tissues. These data raise the possibility that CRISP2 is a MAP3K11-modifying protein or, alternatively, that MAP3K11 acts to phosphorylate CRISP2 during acrosome development.
A polynomial-time algorithm for diagnosability verification of discrete event systems

This paper concerns the problem of diagnosing the occurrence of permanent fault events in partially observed discrete event systems modelled as finite-state automata in a event-based framework. The first step is the verification of the existence of diagnosers (the diagnosability problem) for such systems. We define a necessary and sufficient condition of diagnosability of such systems. The results proposed in this paper allow testing the diagnosability of discrete event systems in an efficient way, i.e. in polynomial time. The diagnosability test is stated in terms of existence of similar cycles of observable events both in the faultless model and in the faulty model.
Crystal structure of the human dual specificity phosphatase 1 catalytic domain

The dual specificity phosphatase DUSP1 was the first mitogen activated protein kinase phosphatase (MKP) to be identified. It dephosphorylates conserved tyrosine and threonine residues in the activation loops of mitogen activated protein kinases ERK2, JNK1 and p38‐alpha. Here, we report the crystal structure of the human DUSP1 catalytic domain at 2.49 Å resolution. Uniquely, the protein was crystallized as an MBP fusion protein in complex with a monobody that binds to MBP. Sulfate ions occupy the phosphotyrosine and putative phosphothreonine binding sites in the DUSP1 catalytic domain.
The Relationship between Education and Occupation Using Fully and Partially Latent Models

Several studies have been carried out to examine the association between education and occupation. These studies were useful for the purpose of intervention and policy making. In this study we examined the relationship between education factor, which includes three indicators: the percentages of population who achieved (primary, secondary and tertiary) and occupation factor (CLASS1, CLASS2 and CLASS3) using fully and partially latent models. The data were collected from the information of 81 districts based on the census conducted in peninsular Malaysia in 1995. The goodness of fit indexes for assumed models were examined. We didn't find significant relationship between educational achievement and occupation factor. This study was composed for a number of path-diagrams to create a picture for socioeconomic status in Malaysia.
Evaluation of cardioprotective effect of aqueous extract of Garcinia indica Linn. fruit rinds on isoprenaline-induced myocardial injury in Wistar albino rats

In the present study, cardioprotective effect of aqueous extract of Garcinia indica Linn. fruit rinds in isoprenaline-induced myocardial infarction in Wistar albino rats was evaluated. In vitro total phenolic, total flavonoid content and 2, 2’-diphenyl-1-picrylhydrazyl hydrate radical scavenging activity was measured. In vivo effect of aqueous extract of G. indica was evaluated in Wistar albino rats by isoprenaline-induced myocardial injury model. Thirty six rats were randomly divided in 6 groups. Rats were treated with G. indica 250 mg/kg and 500 mg/kg doses for 21 days and myocardial injury was produced by subcutaneous injection of isoprenaline 85 mg/kg on day 20 and 21. Carvedilol 1 mg/kg for 21 days served as active control. Electrocardiogram parameters, cardiac injury markers (serum troponin-I, uric acid, lactate dehydrogenase, creatinine kinase-MB, aspartate aminotransferase and alanine aminotransferase), oxidative stress markers (superoxide dismutase, catalase and malondialdehyde level) and histopathological changes were evaluated in each group and compared using appropriate statistical tests. In vitro evaluation of aqueous extract showed significant antioxidant property. Isoprenaline produced significant myocardial ischemia as compared to normal control group (P<0.05). Administration of G. indica in both the doses did not significantly recover the altered electrocardiogram, cardiac injury markers, oxidative stress markers and histopathological myocardial damage as compared to disease control group (P>0.05). The aqueous extract of G. indica was not found to be cardioprotective against myocardial injury. Further study with more sample size and higher dose range may be required to evaluate its cardioprotective effect.
PIVE: Per-Iteration Visualization Environment for Real-Time Interactions with Dimension Reduction and Clustering

One of the key advantages of visual analytics is its capability to leverage both humans's visual perception and the power of computing. A big obstacle in integrating machine learning with visual analytics is its high computing cost. To tackle this problem, this paper presents PIVE (Per-Iteration Visualization Environment) that supports real-time interactive visualization with machine learning. By immediately visualizing the intermediate results from algorithm iterations, PIVE enables users to quickly grasp insights and interact with the intermediate output, which then affects subsequent algorithm iterations. In addition, we propose a widely-applicable interaction methodology that allows efficient incorporation of user feedback into virtually any iterative computational method without introducing additional computational cost. We demonstrate the application of PIVE for various dimension reduction algorithms such as multidimensional scaling and t-SNE and clustering and topic modeling algorithms such as k-means and latent Dirichlet allocation.
Two Methods of Mechanical Noise Reduction of Recorded Speech During Phonation in an MRI device

Two Methods of Mechanical Noise Reduction of Recorded Speech During Phonation in an MRI device The paper presents two methods of noise reduction of speech signal recorded in an MRI device during phonation for the human vocal tract modelling. The applied approach of noise speech signal cleaning is based on cepstral speech analysis and synthesis because the noise is mainly produced by gradient coils, has a mechanical character, and can be processed in spectral domain. Our first noise reduction method is using real cepstrum limitation and clipping the "peaks" corresponding to the harmonic frequencies of mechanical noise. The second method is coming out from substation of the short-time spectra of two signals recorded withal: the first includes speech and noise, and the second consists of noise only. The resulting speech quality was compared by spectrogram and mean periodogram methods.
An adaptive environment based on Moodle with treating of quality of context

Ubiquitous learning (U-Learning) environments collect context information relative to user's preferences and needs, but this information is typically very volatile. On this basis, the Quality of the Context aims at treating this information with the application of the quality parameters. This paper presents a ubiquitous virtual environment, in which three modules (U-SEA, SEDECA and QoC) were developed and integrated with Moodle, and describes the use of a Bootstrap theme to automatically adapt the interface on mobile devices. The results about the integrated modules showed that the UVLEQoC environment operated satisfactorily, based on the assessments made by the group of users who tested the modules and their operation.
Combined Use of Inactivated and Oral Poliovirus Vaccines in Refugee Camps and Surrounding Communities — Kenya, December 2013

Since the launch of the Global Polio Eradication Initiative (GPEI) in 1988, circulation of indigenous wild poliovirus (WPV) has continued without interruption in only three countries: Afghanistan, Nigeria, and Pakistan. During April-December 2013, a polio outbreak caused by WPV type 1 (WPV1) of Nigerian origin resulted in 217 cases in or near the Horn of Africa, including 194 cases in Somalia, 14 cases in Kenya, and nine cases in Ethiopia (all cases were reported as of March 10, 2014). During December 14-18, 2013, Kenya conducted the first-ever campaign providing inactivated poliovirus vaccine (IPV) together with oral poliovirus vaccine (OPV) as part of its outbreak response. The campaign targeted 126,000 children aged ≤59 months who resided in Somali refugee camps and surrounding communities near the Kenya-Somalia border, where most WPV1 cases had been reported, with the aim of increasing population immunity levels to ensure interruption of any residual WPV transmission and prevent spread from potential new importations. A campaign evaluation and vaccination coverage survey demonstrated that combined administration of IPV and OPV in a mass campaign is feasible and can achieve coverage >90%, although combined IPV and OPV campaigns come at a higher cost than OPV-only campaigns and require particular attention to vaccinator training and supervision. Future operational studies could assess the impact on population immunity and the cost-effectiveness of combined IPV and OPV campaigns to accelerate interruption of poliovirus transmission during polio outbreaks and in certain areas in which WPV circulation is endemic.
Adaptive Nonlinear Digital Self-Interference Cancellation for Mobile Inband Full-Duplex Radio: Algorithms and RF Measurements

This article investigates novel adaptive self-interference cancellation solutions and the total integrated cancellation performance of a mobile single-antenna inband full-duplex transceiver. First, novel self-adaptive digital self-interference cancellation algorithms are described, with an emphasis on tracking of time-varying self-interference coupling channel in a mobile device as well as on structural ability to suppress also nonlinear self-interference with highly nonlinear mobile power amplifiers. This leads to an advanced self-adaptive nonlinear digital canceller which utilizes a novel orthogonalization procedure for nonlinear basis functions, together with low-cost LMS-based parameter learning. The achievable self-interference cancellation performance is then evaluated with actual RF measurements using mobile device scale RF components, in particular a highly nonlinear PA. The measurements also incorporate a novel self-adaptive RF cancellation circuit in order to realistically assess the total integrated cancellation performance. The reported results show that highly efficient self-interference cancellation can be achieved also in a mobile device, despite a heavily nonlinear PA and limited computing and hardware resources. The proposed cancellation solutions, when integrated together, show that 100 dB of self-interference can be cancelled using a 20 MHz LTE waveform, while the SI can be attenuated by over 110 dB with a narrower bandwidth of 1.4 MHz, all measured at 2.4 GHz ISM band. Furthermore, these results are achieved using a highly nonlinear transmitter power amplifier and fully adaptive canceller structures which can track a rapidly changing coupling channel in a mobile full-duplex device.
Irrigation Systems for Idaho Agriculture

daho has approximately 4 million acres of irrigated agricultural land. Most of it is in pasture and hay crops, grain crops, potatoes, and sugar beets, in hierarchical order. Table 1 shows the number of irrigated acres in the state by crop for 1994. Nearly all of this land is irrigated by either sprinklers (59 percent) or surface irrigation systems (40 percent), with only a very small amount (less than 1 percent) in micro-irrigation systems (trickle or drip) (table 2). The selection of an irrigation system, or the decision to continue with a gravity system rather than convert to a sprinkler system, is a matter of tradeoffs among the following factors: initial investment costs, operating costs, site factors, and management skills. A relative comparison of these factors is given on pages 4-5. In general, the higher-investment, higher-water-applicationefficiency systems are found in areas where large fields of high-value, water-sensitive crops are grown, or where water supply may be limited or pumping lift is high. Lower-initial-investment surface systems are generally used in short-growing season areas or areas where soil depth or texture limits production. Lack of available threephase electric power and seed production requirements for dry foliage (for disease control) may also dictate the continued use of surface irrigation. In a ideal irrigation system, on a field with uniform soil properties, water is supplied uniformly over the entire area of a field at a rate not to exceed the rate at which water will enter the soil (infiltration rate), and with a frequency and amount to meet the crop need. Since crop water use varies during the year, water application should also vary to just meet this need. Water in excess of crop need should be applied only on Irrigation Systems for Idaho Agriculture
Obstacle avoidance with LGMD neuron: Towards a neuromorphic UAV implementation

We present a neuromorphic adaptation of a spiking neural network model of the locust Lobula Giant Movement Detector (LGMD), which detects objects increasing in size in the field of vision (looming) and can be used to facilitate obstacle avoidance in robotic applications. Our model is constrained by the parameters of a mixed signal analog-digital neuromorphic device, developed by our group, and is driven by the output of a neuromorphic vision sensor. We demonstrate the performance of the model and how it may be used for obstacle avoidance on an unmanned areal vehicle (UAV).
Expose for student research paper In preparation for dependency parse driven composition models for argument facet aware vector space representations of textual units

Large online debates contain redundant arguments and therefore hinder efficient debating. To tackle this problem Boltuzic and Šnajder (2015) proposed to cluster similar arguments and filter only the most representative ones. The Common Round1 project (Uszkoreit et al. 2017) introduces a platform to facilitate large scale online debating with NLP technologies. The authors define the aggregation of the semantic content of debates as one of their major objectives which they intend to achieve by clustering similar arguments. Moreover, Misra, Ecker, and Walker (2016) define the Argument Facet Similarity (AFS) task as the recognition of the semantic similarity of two sentential arguments. To achieve these goals, a semantically consistent similarity measure for arguments is necessary. Frameworks like word2vec (Mikolov et al. 2013) or glove (Pennington, Socher, and Manning 2014) lead to success in many NLP tasks by producing dense embedding vectors for single words. The cosine distance of these word embeddings enables a semantically consistent similarity measure for word tokens. Building on this, Habernal and Gurevych (2015), Boltuzic and Šnajder (2015), and Misra, Ecker, and Walker (2016) use summed or averaged word embeddings for argument similarity measures. However, Misra, Ecker, and Walker (2016) state that averaging all word embeddings may lose too much information in long sentences. Wang and Zong (2017) present an overview of different embedding composition models for phrase representations. They conclude that the recurrent long short-term memory (LSTM) model (Hochreiter and Schmidhuber 1997) just slightly outperforms the additive baseline model in this task. More recently, Tai, Socher, and Manning (2015) introduced the recursive TreeLSTM model which further reduced the vanishing gradient problem as compared to recurrent models by shortening the average distance of entities in the computation graph. The authors use dependency parse trees to construct the neural model and present promising results for the SICK phrase relatedness task2. However, these models are applied to sentences, but not yet to multi-sentence arguments or paragraphs. Additionally, their approach does not use dependency edge type information such as ’nsubj’ (nominal subject) or ’prep’ (preposition).
A Comparison between Voltage and Reactive Power Feedback Schemes of DFIGs for Inter-Area Oscillation Damping Control

Reactive power modulation of wind power plants is an effective way to damp inter-area oscillation in wind power penetrated power systems. For doubly fed induction generator (DFIG) based wind farms, there are two different ways to achieve reactive power modulation: one is via reactive power feedback control, and the other method is via voltage feedback control. While both of the control schemes are feasible, their effectiveness may differ, and there has not been a systematic comparison between them. This paper investigates the differences between these two feedback schemes for inter-area oscillation damping control. The principles of utilizing DFIG for damping control is introduced at first. Then, analytical techniques including the frequency domain analysis, μ -analysis and time domain analysis are used to systematically study the performance of the two control schemes against inter-area oscillation. The robustness of the control schemes with respect to the variety of system operation points is also studied. The results from this paper can provide an insight into the understatement of DFIG reactive modulation against oscillation and guidance for controller design.
Pathogenicity potential of Staphylococcus pseudintermedius strains isolated from canine carriers and from dogs with infection signs

The aim of this study was to compare the pathogenicity potential of Staphylococcus pseudintermedius strains isolated from healthy dogs and dogs with evident symptoms of infection. Nearly all examined strains synthesized β-hemolysin, clumping factor, coagulase, DNase, protein A, and lipase. The only statistically significant intergroup difference pertained to protein A, synthesized more frequently in infected dogs. All strains were positive for siet and lukS/F genes. No sea, seb, sed, see and tst genes were detected. The sec gene was detected in 1/71 (1.4%) strains obtained from a healthy dog and in 2/120 (1.6%) strains from infected animals. The subsequent DNA sequencing analysis revealed that the amplified sec genes in all the S. pseudintermedius isolates were subgrouped into the type SECcanine.