Miracle-dz/UniFAR-FTUs huggingface dataset:
Boolean Matrix Factorization and Noisy Completion via Message Passing

Boolean matrix factorization and Boolean matrix completion from noisy observations are desirable unsupervised data-analysis methods due to their interpretability, but hard to perform due to their NP-hardness. We treat these problems as maximum a posteriori inference problems in a graphical model and present a message passing approach that scales linearly with the number of observations and factors. Our empirical study demonstrates that message passing is able to recover low-rank Boolean matrices, in the boundaries of theoretically possible recovery and compares favorably with state-of-the-art in real-world applications, such collaborative filtering with large-scale Boolean data.
Genetic evidence that the gacA gene encodes the cognate response regulator for the lemA sensor in Pseudomonas syringae

Mutational analysis of the bean-pathogenic Pseudomonas syringae pv. syringae strain B728a has led to the genetic identification of the gacA gene as encoding the response regulator for the unlinked lemA sensor kinase. The analysis of a collection of spontaneous mutants of P. syringae pv. syringae suggested that the gacA gene was involved in lesion formation and the production of protease and syringomycin. The gacA gene originally was identified as a regulator of extracellular antibiotic production by Pseudomonas fluorescens, and the predicted GacA protein is a member of the FixJ family of bacterial response regulators. The sequence of the putative B728a GacA protein revealed 92% identity with the P. fluorescens GacA protein. An insertional mutation within the P. syringae pv. syringae gacA gene abrogated lesion formation on beans, production of extracellular protease, and production of the toxin syringomycin, the same phenotypes affected by a lemA mutation. DNA sequence analysis identified the P. syringae pv. syringae uvrC gene immediately downstream of the gacA gene, an arrangement conserved in P. fluorescens and Escherichia coli. The gacA insertional mutant was sensitive to UV, presumably because of polarity on transcription of the downstream uvrC gene. Southwestern (DNA-protein) analysis revealed that the lemA and gacA genes were required for the full expression of a DNA binding activity.
A low noise sensor interface circuit in CMOS digital process

A low noise interface circuit of MEMS sensor system for ultra-low frequency signal is presented in this paper. The interface circuit in CMOS processes uses chopper technique which greatly reduces 1/f noise and offset voltage of small signal processing circuit. The circuit that has a gain of 63 is fabricated in 0.5um 2P3M CMOS process. The equivalent input noise caused by clock through and charge injection is lower than 1μV. The 3rd order intermodulation distortion is 2.1% when the input signal amplitude is 1mV. The circuit power consumption is 10mW.
ROS-Mediated Autophagy Induced by Dysregulation of Lipid Metabolism Plays a Protective Role in Colorectal Cancer Cells Treated with Gambogic Acid

Gambogic acid (GA), the main active component of gamboge resin, has potent antitumor activity both in vivo and in vitro. However, the underlying molecular mechanisms remain unclear. In this study, we found that GA could initiate autophagy in colorectal cancer cells, and inhibition of the autophagy process accelerated the effect of proliferative inhibition and apoptotic cell death induced by GA, implying a protective role of autophagy. Two-dimensional electrophoresis-based proteomics showed that GA treatment altered the expression of multiple proteins involved in redox signaling and lipid metabolism. Functional studies revealed that GA-induced dysregulation of lipid metabolism could activate 5-lipoxygenase (5-LOX), resulting in intracellular ROS accumulation, followed by inhibition of Akt-mTOR signaling and autophagy initiation. Finally, results using a xenograft model suggested ROS-induced autophagy protect against the antitumor effect of GA. Taken together, these data showed new biological activities of GA against colorectal cancer underlying the protective role of ROS-induced autophagy. This study will provide valuable insights for future studies regarding the anticancer mechanisms of GA.
The Personal Interaction Panel – a Two‐Handed Interface for Augmented Reality

This paper describes the introduction of a new interaction paradigm to augmented reality applications. The everyday tool handling experience of working with pen and notebooks is extended to create a three dimensional two‐handed interface, that supports easy‐to‐understand manipulation tasks in augmented and virtual environments. In the design step we take advantage from the freedom, given by our very low demands on hardware and augment form and functionality to this device. On the basis of examples from object manipulation, augmented research environments and scientific visualization we show the generality of applicability. Although being in the first stages implementation, we consider the wide spectrum of suitability for different purposes.
Automatic Phonemic Transcription and Linguistic Annotation from Known Text with Hidden Markov Models

This paper describes the architecture of a word and phoneme aligner based on Hidden Markov Models (HMMs). It was developed to allow for word, syllable and segment length extraction as part of a feature extraction stage for prosody recognition. From a given orthographic ASCII text and sampled speech data, a label le with phonemes, syllables or words is automatically generated. Linguistic categories coded in the lexicon can also be included in the generated label les.
Scene understanding with discriminative structured prediction

Spatial priors play crucial roles in many high-level vision tasks, e.g. scene understanding. Usually, learning spatial priors relies on training a structured output model. In this paper, two special cases of discriminative structured output model, i.e. conditional random fields (CRFs) and max-margin Markov networks (M3N), are demonstrated to perform image scene understanding. The two models are empirically compared in a fair manner, i.e. using the common feature representation and the same optimization algorithm. Particularly, we adopt online exponentiated gradient (EG) algorithm to solve the convex duals of both models. We describe the general procedure of EG algorithm and present a two-stage training procedure to overcome the degeneration of EG when exact inference is intractable. Experiments on a large scale image region annotation task are carried out. The results show that both models yield encouraging results but CRFs slightly outperforms M3N.
Nonlinear control for a diesel engine: A CLF-based approach

Abstract In this paper, we propose a control Lyapunov function based on a nonlinear controller for a turbocharged diesel engine. A model-based approach is used which predicts the experimentally observed engine performance for a biodiesel. The basic idea is to develop an inverse optimal control and to employ a Lyapunov function in order to achieve good performances. The obtained controller gain guarantees the global convergence of the system and regulates the flows for the variable geometry turbocharger as well as exhaust gas recirculation systems in order to minimize the NOx emission and the smoke of a biodiesel engine. Simulation of the control performances based on professional software and experimental results show the effectiveness of this approach.
Syntactic pattern analysis of 5'-splice site sequences of mRNA precursors in higher eukaryote genes

The signals which direct the excision of introns from eukaryotic pre-mRNA are not yet well understood. In order to define the signals for 5'-splice sites of mRNA splicing, nucleotide sequences including 5'-splice junctions of mammalian pre-mRNAs are analysed by means of syntactic pattern analysis. Taking this approach, we infer the grammatical rules which specify 5'-splice sites and construct a finite automaton which is the recognizer of the nucleotide sequences at 5'-splice sites. By scanning the automaton along nucleotide sequences, we can identify the positions of 5'-splice junctions with a degree of discrimination of up to 94-97% in the known genes, while the degree of prediction is in the range 50-55% in new genes.
Reverse engineering and identification in systems biology: strategies, perspectives and challenges

The interplay of mathematical modelling with experiments is one of the central elements in systems biology. The aim of reverse engineering is to infer, analyse and understand, through this interplay, the functional and regulatory mechanisms of biological systems. Reverse engineering is not exclusive of systems biology and has been studied in different areas, such as inverse problem theory, machine learning, nonlinear physics, (bio)chemical kinetics, control theory and optimization, among others. However, it seems that many of these areas have been relatively closed to outsiders. In this contribution, we aim to compare and highlight the different perspectives and contributions from these fields, with emphasis on two key questions: (i) why are reverse engineering problems so hard to solve, and (ii) what methods are available for the particular problems arising from systems biology?
Lipid Nanocarriers-Enabled Delivery of Antibiotics and Antimicrobial Adjuvants to Overcome Bacterial Biofilms

The opportunistic bacteria growing in biofilms play a decisive role in the pathogenesis of chronic infectious diseases. Biofilm-dwelling bacteria behave differently than planktonic bacteria and are likely to increase resistance and tolerance to antimicrobial therapeutics. Antimicrobial adjuvants have emerged as a promising strategy to combat antimicrobial resistance (AMR) and restore the efficacy of existing antibiotics. A combination of antibiotics and potential antimicrobial adjuvants, (e.g., extracellular polymeric substance (EPS)-degrading enzymes and quorum sensing inhibitors (QSI) can improve the effects of antibiotics and potentially reduce bacterial resistance). In addition, encapsulation of antimicrobials within nanoparticulate systems can improve their stability and their delivery into biofilms. Lipid nanocarriers (LNCs) have been established as having the potential to improve the efficacy of existing antibiotics in combination with antimicrobial adjuvants. Among them, liquid crystal nanoparticles (LCNPs), liposomes, solid lipid nanoparticles (SLNs), and nanostructured lipid carriers (NLCs) are promising due to their superior properties compared to traditional formulations, including their greater biocompatibility, higher drug loading capacity, drug protection from chemical or enzymatic degradation, controlled drug release, targeted delivery, ease of preparation, and scale-up feasibility. This article reviews the recent advances in developing various LNCs to co-deliver some well-studied antimicrobial adjuvants combined with antibiotics from different classes. The efficacy of various combination treatments is compared against bacterial biofilms, and synergistic therapeutics that deserve further investigation are also highlighted. This review identifies promising LNCs for the delivery of combination therapies that are in recent development. It discusses how LNC-enabled co-delivery of antibiotics and adjuvants can advance current clinical antimicrobial treatments, leading to innovative products, enabling the reuse of antibiotics, and providing opportunities for saving millions of lives from bacterial infections.
Orthogonal Rendezvous Routing Protocol for Wireless Mesh Networks

Routing in multi-hop wireless networks involves the indirection from a persistent name (or ID) to a locator. Concepts such as coordinate space embedding help reduce the number and dynamism complexity of bindings and state needed for this indirection. Routing protocols which do not use such concepts often tend to flood packets during route discovery or dissemination, and hence have limited scalability. In this paper, we introduce Orthogonal Rendezvous Routing Protocol (ORRP) for meshed wireless networks. ORRP is a lightweight-but-scalable routing protocol utilizing directional communications (such as directional antennas or free-space-optical transceivers) to relax information requirements such as coordinate space embedding and node localization. The ORRP source and ORRP destination send route discovery and route dissemination packets respectively in locally-chosen orthogonal directions. Connectivity happens when these paths intersect (i.e., rendezvous). We show that ORRP achieves connectivity with high probability even in sparse networks with voids. ORRP scales well without imposing DHT-like graph structures (eg: trees, rings, torus etc). The total state information required is O(N3/2) for N-node networks, and the state is uniformly distributed. ORRP does not resort to flooding either in route discovery or dissemination. The price paid by ORRP is suboptimality in terms of path stretch compared to the shortest path; however we characterize the average penalty and find that it is not severe.
Refinement of Intraocular Pressure Measurements made by Ocular Response Analyzer following Laser in Situ Keratomileusis using M2 90 Moria Microkeratome for Egyptian Myopic and Astigmatic Patients

Introduction The Goldmann applanation tonometer readings were noted to be markedly reduced after Lasik surgery using a thin flap technique which is widely used nowadays, to correct a wide range of myopia and astigmatism. The Ocular Response Analyzer (ORA) is considered one of the important tools for refinement of Intraocular Pressure (IOP) measurements. The aim of this study is to evaluate and refine ORA measurements for IOP changes post- M2 90 Moria microkeratome Lasik procedure for Egyptian myopic and astigmatic patients trying to aid in glaucoma diagnosis and management. Methods Thirty-five eyes of nineteen Egyptian patients with myopia or myopic astigmatism who had undergone Lasik procedure using M2 90 Moria microkeratome were included in this consecutive case series study. All cases were subjected to full ophthalmological examination including uncorrected and best corrected visual acuity, refraction, slit lamp examination, Scheimpflug imaging and ORA (Reichert Ophthalmic Instruments, Inc., Buffalo, NY, USA). The refractive errors were measured using an auto refractometer and were confirmed by trial. For the ocular response analyzer, the Goldmann-correlated IOP measurement (IOPg) which simulates IOP measured by Goldmann tonometer and the Corneal-Compensated Intraocular Pressure (IOPcc) that takes corneal biomechanical properties into consideration were reported as well as the Corneal Hysteresis (CH) and the Corneal Resistance Factor (CRF). Cases were examined preoperatively and again about one month after Lasik, after stabilization of eye condition. The collected data were tabulated and analysed with the suitable statistical methods. The mean values and standard deviation were calculated for quantitative data. Comparison tests (t-test) and correlation tests (Pearson) were also performed. Results In our study, involving M2 90 Moria microkeratome Lasik procedure, a highly significant post-Lasik reduction in IOPg (t-test = 8.62 (p<0.01), and a statistically significant reduction in IOPcc (t-test = 3.37 (p<0.05) by ocular response analyzer. The average post-Lasik reduction in IOP in mmHg was 4.84±2.82 for IOPg and 2.23±3.51for IOPcc. A statistically significant correlation (p<0.05) existed between post-Lasik reduction of IOPg and ablation depth as well as preoperative spherical equivalent. A non-significant correlation existed between post-Lasik reduction of IOPcc and both of ablation depth and preoperative spherical equivalent. Conclusions Following Lasik procedure using M2 90 Moria microkeratome, the IOPcc values by ORA were closer to the preoperative values than the IOPg values and the reduction of IOPcc values was not affected by ablation depth (i.e. preoperative spherical equivalent). Therefore, it is advisable to use the IOPcc values by ORA when evaluating post-Lasik patients for glaucoma diagnosis and management, but with the addition of the average value for post-Lasik reduction which in the study was 2.23±3.51mmHg.
Secure data provenance compression using arithmetic coding in wireless sensor networks

Since data are originated and processed by multiple agents in wireless sensor networks, data provenance plays an important role for assuring data trustworthiness. However, the size of the provenance tends to increase at a higher rate as it is transmitted from the source to the base station and is processed by many intermediate nodes. Due to bandwidth and energy limitations of wireless sensor networks, such increasing of provenance size slows down the network and depletes the energy of sensor nodes. Therefore, compression of data provenance is an essential requirement. Existing lossy compression schemes based on Bloom filters or probabilistic packet marking approaches have high error rates in provenance-recovery. In this paper, we address this problem and propose a distributed and lossless arithmetic coding based compression technique which achieves a compression ratio higher than that of existing techniques and also close to Shannon's entropy bound. Unlike other provenance schemes, the most interesting characteristic of our scheme is that the provenance size is not directly proportional to the number of hops, but to the occurrence probabilities of the nodes that are on a packet's path. We also ensure the confidentiality, integrity, and freshness of provenance to prevent malicious nodes from compromising the security of data provenance. Finally, the simulation and testbed results provide a strong evidence for the claims in the paper.
On topology control and non-uniform node deployment in ad hoc networks

Topology control has been established as an efficient technique for improving the properties of wireless multi-hop networks. In this paper we first analyze the impact of non-uniform node placement on the effectiveness of traditional and well established topology control approaches that preserve connectivity with high probability, thus revealing and demonstrating their inefficiency in properly maintaining connectivity in the general case. Then, we propose a randomized topology control approach that provides significant improvements in percentage connectivity guarantees under arbitrary and more realistic node deployments. The proposed approach, referred to as Nearest Random Neighbors (NRN), is compared to the K-Neigh technique, one of the dominant Network layer topology control protocols. As opposed to K-Neigh, the NRN mechanism asserts acceptable network connectivity probabilities, even in cases of highly skewed node distributions, while its performance with respect to the average physical node degree remains stable and close to K-Neigh, even as the network density increases dramatically.
The Arabidopsis Stem Cell Factor POLTERGEIST Is Membrane Localized and Phospholipid Stimulated[W][OA]

This work explores how the shoot and root stem cell promoting factors POLTERGEIST (POL) and PLL1 are regulated at the cellular level. Specifically, this study reveals that both of these protein phosphatase type 2C proteins are membrane localized via acylation and that phospholipid binding stimulates POL activity. Stem cell maintenance and differentiation are tightly regulated in multicellular organisms. In plants, proper control of the stem cell populations is critical for extensive postembryonic organogenesis. The Arabidopsis thaliana protein phosphatase type 2C proteins POLTERGEIST (POL) and PLL1 are essential for maintenance of both the root and shoot stem cells. Specifically, POL and PLL1 are required for proper specification of key asymmetric cell divisions during stem cell initiation and maintenance. POL and PLL1 are known to be integral components of the CLE/WOX signaling pathways, but the location and mechanisms by which POL and PLL1 are regulated within these pathways are unclear. Here, we show that POL and PLL1 are dual-acylated plasma membrane proteins whose membrane localization is required for proper function. Furthermore, this localization places POL and PLL1 in proximity of the upstream plasma membrane receptors that regulate their activity. Additionally, we find that POL and PLL1 directly bind to multiple lipids and that POL is catalytically activated by phosphatidylinositol (4) phosphate [PI(4)P] in vitro. Based on these results, we propose that the upstream receptors in the CLE/WOX signaling pathways may function to either limit PI(4)P availability or antagonize PI(4)P stimulation of POL/PLL1. Significantly, the findings presented here suggest that phospholipids play an important role in promoting stem cell specification.
Immunocytochemical Study of Endocytotic Structures Accumulated in HeLa Cells Transformed with a Temperature-sensitive Mutant of Dynamin

Dynamin is a 100-kD GTPase, which is required for clathrin-mediated endocytosis. Recent studies have revealed that dynamin is closely involved in clathrin-coated vesicle formation. In this study we investigated the ultrastructure of endocytotic structures accumulated in HeLa cells that were transformed with a temperature-sensitive (ts) mutant of dynamin to clarify which step was blocked in dynts cells. Endocytosis of transferrin receptors was restricted at the level of surface-connected membrane structures. Tubular and vesicular membrane invaginations were accumulated in the cells' peripheral regions, suggesting that the endocytosis was blocked just before the pinching-off steps in coated vesicle formation. The “collared” tubes, which were reported to be localized in nerve terminals in shibirets1 flies and GTPγS-treated synaptosomes, were not observed in the dynts cells even at nonpermissive temperature. The distribution pattern of dynamin in deeply invaginated coated pits in dynts cells was similar to that in dynwt cells but not to that in dynK44A cells, which are other endocytosis-defective mutant cells. These morphological data suggest that dynts blocked the pinching-off steps in clathrin-coated vesicle formation, which may be caused by a different mechanism from that of dynK44A cells.
Perceived Stress as a Stimulant of Social Undermining in the Virtual Workplace: A Serial Mediation Model

Interpersonal disagreement among employees at the workplace is an important predictor of perceived stress in general and for virtual and digitally connected workplace in particular. Such perceived stress may potentially lead the employees towards social undermining. This study was a quantitative study and data was collected from different organizations which were primarily based on information and communication technology (ICT) based systems for testing a serial mediation model containing task conflict and relationship conflict as serial mediators. Statistical analysis had shown a significant indirect effect on outcome variable of social undermining by the serial mediators. Discussion has been made with reference to contextual factors such as those in the context of mindfulness theory and other factors that might have impacted this relationship of variables. Such a relationship of variables has not been tested on employees working in virtual and digital setup where psychological contract also plays a part towards conflict generation and its handling leading associated with job stress. Finally, this paper recommends useful future research direction for the contemporary researchers.