Miracle-dz/UniFAR-FTUs huggingface dataset:
Combining Random Gene Fission and Rational Gene Fusion To Discover Near-Infrared Fluorescent Protein Fragments That Report on Protein–Protein Interactions

Gene fission can convert monomeric proteins into two-piece catalysts, reporters, and transcription factors for systems and synthetic biology. However, some proteins can be challenging to fragment without disrupting function, such as near-infrared fluorescent protein (IFP). We describe a directed evolution strategy that can overcome this challenge by randomly fragmenting proteins and concomitantly fusing the protein fragments to pairs of proteins or peptides that associate. We used this method to create libraries that express fragmented IFP as fusions to a pair of associating peptides (IAAL-E3 and IAAL-K3) and proteins (CheA and CheY) and screened for fragmented IFP with detectable near-infrared fluorescence. Thirteen novel fragmented IFPs were identified, all of which arose from backbone fission proximal to the interdomain linker. Either the IAAL-E3 and IAAL-K3 peptides or CheA and CheY proteins could assist with IFP fragment complementation, although the IAAL-E3 and IAAL-K3 peptides consistently yielded higher fluorescence. These results demonstrate how random gene fission can be coupled to rational gene fusion to create libraries enriched in fragmented proteins with AND gate logic that is dependent upon a protein–protein interaction, and they suggest that these near-infrared fluorescent protein fragments will be suitable as reporters for pairs of promoters and protein–protein interactions within whole animals.
Design of a Biomimetic Directional Microphone Diaphragm

A miniature silicon condenser microphone diaphragm has been designed that exhibits good predicted directionality, sensitivity, and reliability. The design was based on the structure of a fly’s ear (Ormia ochracea) that has highly directional hearing through mechanical coupling of the eardrums. The diaphragm that is 1mm × 2mm × 20 microns is intended to be fabricated out of polysilicon through microelectromechanical micromachining. It was designed through the finite-element method in ANSYS in order to build the necessary mode shapes and frequencies into the mechanical behavior of the design. Through postprocessing of the ANSYS data, the diaphragm’s response to an arbitrary sound source, sensitivity, robustness, and Articulation Index - Directivity Index (AI-DI) were predicted. The design should yield a sensitivity as high as 100 mV/Pa, an AI-DI of 4.764 with Directivity Index as high as 6 between 1.5 and 5 kHz. The diaphragm structure was predicted be able to withstand a sound pressure level of 151.74 dB. The sound level that would result in collapse of the capacitive sensor is 129.9 dB. The equivalent sound level due to the self-noise of the microphone is predicted to be 30.8 dBA.
Working Memory Architecture and its Implications for Hypertext Design : Insight from Deaf Signer Users Research

Starting from models of working memory and hypertext navigation, this research focused on how the specific demands of hypertext systems could be adapted to fulfill the memory peculiarities of deaf signer users. We manipulated the Verbal and Visuospatial storage demands of a hypertext information retrieval task. The results showed that differences in accuracy, response time, and lostness between deaf signers and hearing non-signers are smaller in spatial-demanding hypertext compared to verbal-demanding hypertext structure. In addition, independently of Web demands, good reader-users (both hearing and deaf) were better than low readers. These results suggest design guidelines of web accessibility for deaf people. In the theoretical plane, the data could support the hypothesis that the effect of SL use over WM could be generalized to others visuo-spatial tasks which are non-exclusively linguistic (Emmorey, 1998, 2002) as hypertext navigation.
Interface, interaction and interactivity: understanding ImpaCT of technology in classroom from a Cultural Historical Activity Theory perspective

Information and communication input/output (ICIO) occur through the orchestration of technical interactivity and pedagogical interactivity. While technologies in classrooms support learning these elements are considered the key to successfully integrating technology in class (Beauchamp & Kennewell, 2013). Therefore, it is important to first understand what these elements are. Technical Interactivity in this context means the exchange of information and communication, among participants in the process of teaching and learning, that is facilitated by access to technology; in this case the IWB. There is a two-way flow between the technology and its users (Higgins, Beauchamp, & Miller, 2007; H. Smith, Higgins, Wall, & Miller, 2005). The presentation and touch features of the IWB provide a unique and enhanced technical interactivity environment that has not been previously possible with any other technology. Kennewell (2001) argues that it is not only the presentation and touch features of the IWB that should be considered when thinking about technical interactivity. There are further technical features of IWB systems, both at the hardware and software level, that add to the uniqueness of the environment and may provide distinctive learning opportunities. The other aspect of ICIO in a classroom is Pedagogical interactivity. In this context it means information and communications between teacher and learners, and learner and learners, to achieve educational goals (Higgins et al., 2007; H. Smith et al., 2005).
Exploiting the Saturation Effect in Automatic Random Testing of Android Applications

Monkey Fuzz Testing (MFT), a form of random testing, continues to gain popularity to test Android apps because of its ease of use. (Untrained) programmers use MFT tools to fully automatically detect certain classes of faults in apps. A challenge for these tools is the lack of a stopping criterion -- programmers currently typically stop these tools when they run out of time. In this paper, we use the notion of the Saturation Effect of an MFT tool on an app under test to define a stopping criterion, parameterized by the app's preconditions and the tool's configurations. We have implemented our approach in the Android Ripper MFT tool. We experimentally report results on 18 real Android app subjects. We show that the saturation effect is able to stop testing when test adequacy has been achieved without wasting test cycles.
Data-driven pronunciation modeling for ASR using acoustic subword units

We describe a method to model pronunciation variation for ASR in a data-driven way, namely by use of automatically derived acoustic subword units. The inventory of units is designed so as to produce maximal separable pronunciation variants of words while at the same time only the most important variants for the particular application are trained. In doing so, the optimal number of variants per word is determined iteratively. All this is accomplished (almost) fully automatically by use of a state splitting algorithm and a variant distance measure. Compared to a baseline system using triphones as subword units and with minimal pronunciation variants, this method achieved a relative improvement of the word error rate by 10%.
Qualitative modelling of regulated metabolic pathways: application to the tryptophan biosynthesis in E.Coli

MOTIVATION The integrated dynamical modelling of mixed metabolic/genetic networks constitutes one of the challenges of systems biology. Furthermore, as most of available data about genetic and metabolic regulations are qualitative, there is a pressing need for rigorous qualitative mathematical approaches. RESULTS On the basis of two established formalisms, the logical modelling of genetic regulatory networks and the Petri net modelling of metabolic networks, we propose a systematic approach for the modelling of regulated metabolic networks. This approach leans on previous work defining a systematic procedure to translate logical regulatory graphs into standard (discrete) Petri nets (PNs). This approach is illustrated by the qualitative modelling of the biosynthesis of tryptophan (Trp) in Escherichia coli, taking into account two types of regulatory feedbacks: the direct inhibition of the first enzyme of the pathway by the final product of the pathway, and the transcriptional inhibition of the Trp operon by the Trp-repressor complex. On the basis of this integrated PN model, we further indicate how available dynamical analysis tools can be applied to obtain significant insights in the behaviour of the system. AVAILABILITY The software GINsim for the logical modelling of genetic regulatory networks together with the PN model of the regulated Trp biosynthesis pathway are available at: http://gin.univ-mrs.fr/GINsim.
Poster: applying unsupervised context-based analysis for detecting unauthorized data disclosure

In this paper, we propose a new unsupervised approach for identifying suspicious access to sensitive relational data. In the proposed method, a tree-like model encapsulates the characteristics of the result-set (i.e., data) that the user normally access within each possible context. During the detection phase, result-sets are examined against the induced model and a similarity score is derived.
A subtype-specific peptide-based enzyme immunoassay for detection of antibodies to the G protein of human respiratory syncytial virus is more sensitive than routine serological tests

Peptides deduced from the central conserved region (residues 158 to 189) of protein G of human respiratory syncytial virus (HRSV) subtypes A and B were used as antigens in subtype-specific enzyme-linked immunosorbent assays (G-peptide ELISAs). These G-peptide ELISAs were compared with seven other serological assays to detect HRSV infection: ELISAs based on complete protein G, on fusion protein F, and on nucleoprotein N; a complement fixation assay; a virus neutralization test; and ELISAs for the detection of immunoglobulin A (IgA) or IgM antibodies specific for HRSV. In paired serum samples from patients with HRSV infection, more infections were diagnosed by the G-peptide ELISA (67%) than by all other serological tests combined (48%). Furthermore, for 16 of 18 patients (89%), the G-peptide ELISAs were able to differentiate between antibodies against HRSV subtypes A and B. This study shows that peptides corresponding to the central conserved region of the attachment protein G of HRSV can successfully be used as antigens in immunoassays. The G-peptide ELISA appeared to be more sensitive than conventional tests for the detection of HRSV antibody titer rises.
Granulocyte Stimulating Factor Attenuates Hypoxic-ischemic Brain Injury by Inhibiting Apoptosis in Neonatal Rats

Purpose This study was undertaken to determine the neuroprotective effect of granulocyte stimulating factor (G-CSF) on neonatal hypoxic-ischemic brain injury. Materials and Methods Seven-day-old male newborn rat pups were subjected to 110 minutes of 8% oxygen following a unilateral carotid artery ligation. Apoptosis was identified by performing terminal deoxynucleotidyl transferase-mediated dUTP nick end-labeling (TUNEL) staining and flow cytometry with a combination of fluorescinated annexin V and propidium iodide (PI) and JC-1 (5,5',6,6'-tetrachloro-1,1',3,3'-tetraethylbenzimidazolyl-carbocyanine iodide). The extent of cerebral infarction was evaluated at 2 weeks after recovery. Results With a single dose (50 µg/ kg) of G-CSF treatment immediately after hypoxic-ischemic insult, hypoxia-ischemia induced increase in TUNEL-positive cells, annexinV+/PI-and JC-1 positive apoptotic cells in the ipsilateral cerebral cortex was significantly reduced at 24 hours, measured by flow cytometry, and the extent of cerebral infarction at 2 weeks after recovery was also significantly attenuated compared to the hypoxia-ischemia control group. Conclusion Our data suggest that G-CSF is neuroprotective by inhibiting apoptosis, thereby reducing the ensuing cerebral infarction in a newborn rat pup model of cerebral hypoxia-ischemia (HI).
Efficient Gröbner Basis Reductions for Formal Verification of Galois Field Arithmetic Circuits

Galois field arithmetic is a critical component in communication and security-related hardware, requiring dedicated arithmetic architectures for better performance. In many Galois field applications, such as cryptography, the data-path size in the circuits can be very large. Formal verification of such circuits is beyond the capabilities of contemporary verification techniques. This paper addresses formal verification of combinational arithmetic circuits over Galois fields of the type F2k using a computer-algebra/algebraic-geometry-based approach. The verification problem is formulated as membership testing of a given specification polynomial in a corresponding ideal generated by the circuit constraints. Ideal membership testing requires the computation of a Gröbner basis, which is computationally very expensive. To overcome this limitation, we analyze the circuit topology and derive a term order to represent the polynomials. Subsequently, using the theory of Gröbner bases over F2k, we show that this term order renders the set of polynomials itself a minimal Gröbner basis of this ideal. Consequently, the verification test reduces to a much simpler case of Gröbner basis reduction via polynomial division, significantly enhancing verification efficiency. To further improve our approach, we exploit the concepts presented in the F4 algorithm for Gröbner basis, and show that the verification test can be formulated as Gaussian elimination on a matrix representation of the problem. Finally, we demonstrate the ability of our approach to verify the correctness of, and detect bugs in, up to 163-bit circuits in F2163-whereas verification utilizing contemporary techniques proves infeasible.
Opportunities and Challenges in OFDMA-Based Cellular Relay Networks: A Radio Resource Management Perspective

The opportunities and flexibility in relay networks and orthogonal frequency-division multiple access (OFDMA) make the combination a suitable candidate network and air-interface technology for providing reliable and ubiquitous high-data-rate coverage in next-generation cellular networks. Advanced and intelligent radio resource management (RRM) schemes are known to be crucial toward harnessing these opportunities in future OFDMA-based relay-enhanced cellular networks. However, it is not very clear how to address the new RRM challenges (such as enabling distributed algorithms, intra-cell/inter-cell routing, intense and dynamic co-channel interference (CCI), and feedback overhead) in such complex environments comprising a plethora of relay stations (RSs) of different functionalities and characteristics. Employment of conventional RRM schemes in such networks will highly be inefficient if not infeasible. The next-generation networks are required to meet the expectations of all wireless users, irrespective of their locations. High-data-rate connectivity, mobility, and reliability, among other features, are examples of these expectations. Therefore, fairness is a critical performance aspect that has to be taken into account in the design of prospective RRM schemes. This paper reviews some of the prominent challenges involved in migrating from the conventional cellular architecture to the relay-based type and discusses how intelligent RRM schemes can exploit the opportunities in relay-enhanced OFDMA-based cellular networks. We identify the role of multiantenna systems and explore the current approaches in literature to extend the conventional schedulers to next-generation relay networks. This paper also highlights the fairness aspect in such networks in the light of the recent literature, provides some example fairness metrics, and compares the performances of some representative algorithms.
Fast Label Embeddings for Extremely Large Output Spaces

Many modern multiclass and multilabel problems are characterized by increasingly large output spaces. For these problems, label embeddings have been shown to be a useful primitive that can improve computational and statistical efficiency. In this work we utilize a correspondence between rank constrained estimation and low dimensional label embeddings that uncovers a fast label embedding algorithm which works in both the multiclass and multilabel settings. The result is a randomized algorithm for partial least squares, whose running time is exponentially faster than naive algorithms. We demonstrate our techniques on two large-scale public datasets, from the Large Scale Hierarchical Text Challenge and the Open Directory Project, where we obtain state of the art results.
Automatic loop shaping of QFT robust controller for load frequency control via nonlinear quadratic inequalities

The large scale power systems are liable to performance deterioration due to the presence of sudden small load perturbations and parameter uncertainties. Due to this, modern control aspects are very important in Load Frequency Control (LFC). This paper presents a robust load frequency controller design based on Quantitative Feedback Theory (QFT). QFT is an engineering control design methodology that explicitly emphasizes the use of feedback to simultaneously and quantitatively reduce the effect of plant uncertainty and satisfy performance specifications. This new controller method not only handles the parametric uncertainty in power system, but also covers a wide range of load changes. This paper also presents automatic loop shaping phase in the QFT design, inorder to synthesize an optimal controller.
Prognostic value of combination of preoperative platelet count and mean platelet volume in patients with resectable non-small cell lung cancer

The aim of the present study was to investigate the prognostic value of the combination of preoperative platelet count (PLT) and mean platelet volume (MPV) in patients with primary operable non-small cell lung cancer (NSCLC). We retrospectively analysed data from 546 patients with NSCLC who underwent complete resection at our institution from 2006 to 2010. Patients’ clinical characteristics and laboratory test data at initial diagnosis were collected. Both preoperative PLT and MPV (COP-MPV) were calculated on the basis of the data obtained using the recommended cut-off values of 300 × 109 L−1 and 11.0 fL, respectively. Patients with both an elevated PLT (≥300× 109 L−1) and a decreased MPV (<11.0 fL) were assigned a score of 2, and patients showing one or neither were allocated a score of 1 or 0, respectively. Multivariate analysis of the 9 clinical laboratory variables selected by univariate analysis revealed that preoperative COP-MPV was a significantly independent prognostic factor for overall survival (OS) (hazard ratio, 1.775; 95% confidence interval, 1.500–2.101; P< 0.001) and disease-free survival (DFS) (hazard ratio, 1.719; 95% confidence interval, 1.454–2.033; P< 0.001). In subgroup analyses for tumour pathological stage (I/II/IIIA) patients, we found that the level of COP-MPV was significantly associated with OS and DFS in each subgroup (P< 0.001, P< 0.001, P<0.001 for OS and P<0.001, P< 0.001, P=0.001 for DFS, respectively). In conclusion, the preoperative COP-MPV is a promising predictor of postoperative survival in patients with NSCLC and could classify these patients into three independent groups before surgery.
Neuraxial anesthesia for cardiac surgery: thoracic epidural and high spinal anesthesia - why is it different?

Anesthesiologists can offer much more then stable blood pressure and heart rate in the intraoperative period. By choosing appropriate anesthetic techniques they can tremendously influence perioperative stress. This may positively impact on the overall surgical outcome. One of the most intriguing aspects of neuraxial anesthesia is its ability to attenuate the stress response to surgery. At present there is no agreement on the clinical importance of such a response but there is substantial indirect evidence that it may play an important role in a patient’s outcome. Neuraxial anesthesia supplemented by general anesthesia is justified and can be safely used in cardiac surgery. The authors of this expert opinion prefer spinal anesthesia to thoracic epidural anesthesia and have been using it routinely for the last 20 years without any neurological complications. The risk of spinal hematoma from a 27G spinal needle prior to full heparinization is unknown but in our opinion is remote. Both epidural and spinal techniques can and should have a place in modern cardiac anesthesia practice and should be further investigated.
Differences in the Profile, Treatment, and Prognosis of Patients With Cardiogenic Shock by Myocardial Infarction Classification: A Report From NCDR

Background— Cardiogenic shock is a deadly complication of an acute myocardial infarction (MI). We sought to characterize differences in patient features, treatments, and outcomes of cardiogenic shock by MI classification: ST–segment-elevation MI (STEMI) versus non–ST-segment elevation MI (NSTEMI). Methods and Results— We compared differences in care by the shock status of 235 541 patients with STEMI and NSTEMI treated at 392 US hospitals from 2007 to 2011. Cardiogenic shock occurred in 12.2% of patients with STEMI versus 4.3% of patients with NSTEMI. Compared with STEMI shock, NSTEMI shock was more likely in patients who were older and predominantly women; had diabetes mellitus, hypertension, previous heart failure, MI, or peripheral arterial disease; and who received coronary artery bypass grafting (11.6% versus 21.2%; P<0.0001) but less likely to have received percutaneous coronary intervention (84.2% versus 35.3%; P<0.0001). Compared with patients with STEMI presenting with shock at admission, patients with NSTEMI presenting with shock had longer delays to percutaneous coronary intervention (1.2 versus 3.2 hours) and coronary artery bypass grafting (7.9 versus 55.9 hours). Cardiogenic shock in patients with STEMI was associated with a lower mortality risk (33.1% shock versus 2.0% no shock; adjusted odds ratio, 14.1; 95% confidence interval, 13.0–15.4; interaction P value <0.0001) compared with patients with NSTEMI (40.8% shock versus 2.3% no shock, odds ratio, 19.0; 95% confidence interval, 17.1–21.2). Conclusions— Cardiogenic shock is associated with high mortality in patients with STEMI and NSTEMI. However, urgent revascularization is more commonly pursued in patients with STEMI presenting with shock than in patients with NSTEMI. More research is needed to improve the outcomes for patients with MI presenting with shock, particularly those presenting with NSTEMI.
Particle filter-model predictive control of quadcopters

In recent years, extensive research has been conducted on the design and control of unmanned aerial vehicles having multiple propellers, called multicopters (especially quad-copters, which has four propellers). In this paper, we propose a method for applying particle filter-model predictive control that can take disturbance and measurement noise into consideration explicitly to the flight control of a quadcopter. Moreover, the validity of the proposed method is verified by simulation.