Miracle-dz/UniFAR-FTUs huggingface dataset:
Analytical and numerical Lyapunov functions for SISO linear control systems with first‐order reset elements

In this paper we provide analytical and numerical Lyapunov functions that prove stability and performance of a First‐order Reset Element (FORE) in feedback interconnection with a SISO linear plant. The Lyapunov functions also allow to establish finite gain ℒ︁2 stability from a disturbance input acting at the input of the plant to the plant output. ℒ︁2 stability is established by giving a bound on the corresponding ℒ︁2 gains. The proof of stability and performance is carried out by showing that the Lyapunov functions constructed here satisfy the sufficient conditions in the main results of Nešić et al. (Automatica 2008; 44(8):2019–2026). In the paper we also point out and illustrate via a counterexample an analysis subtlety overlooked in the preliminary results of Zaccarian et al. (American Control Conference, Portland, OR, U.S.A., 2005). Copyright © 2010 John Wiley & Sons, Ltd.
Transcriptional repressors: multifaceted regulators of gene expression

Through decades of research it has been established that some chromatin-modifying proteins can repress transcription, and thus are generally termed ‘repressors’. Although classic repressors undoubtedly silence transcription, genome-wide studies have shown that many repressors are associated with actively transcribed loci and that this is a widespread phenomenon. Here, we review the evidence for the presence of repressors at actively transcribed regions and assess what roles they might be playing. We propose that the modulation of expression levels by chromatin-modifying, co-repressor complexes provides transcriptional fine-tuning that drives development.
Adaptively supported adaptability

This paper presents an adaptive and adaptable system and its evaluation. The system is based on a commercial spreadsheet application and provides adaptation opportunities for defining a user- and task-specific user interface (new menu entries and key shortcuts for subrouting names and parameters, changing default parameters). The development following a design-evaluation-redesign approach has shown that adaptations are accepted if the user has the opportunity to control their timing and content. This does not necessarily mean that the adaptation is initiated and performed by the user alone (adaptability). On the contrary, the strictly user-controlled adaptation is too demanding for the user. The paper shows how the user's own adaptations can be supported by the system by initial adaptive suggestions showing the rationale of adaptations and the way to perform them.
Some Notes on the Gerstmann Syndrome

IN SPITE OF an extensive bibliography on the syndrome of finger agnosia, disorientation for right and left, agraphia, and acalculia, and of the virtually universal recognition of it as a well-defined neurologic symptom-complex resulting from localized involvement of the parieto-occipital region of the dominant hemisphere, there are still misconceptions about the syndrome, as evidenced by an article recently published in this journal. ’ Consequently, I would like to present once more the clinicalphenomenologic definition of the syndrome and its associated features and to review the subject briefly in the light of present day experience. In a series of papers? and lectures during the course of many years, I have stated that finger agnosia, first described and so designated by me in 1924,z is a disorder of the body image proper. It consists in a primary disturbance or loss of ability to recognize, identify, differentiate, name, select, indicate, and orient as to the individual fingers of either hand, the patient’s own, as well as those of other persons. Subsequent to this gnostic disorientation with respect to the fingers, restriction in their separate kinetic realization occurs not infrequently. It is characteristically associated with lack of recognition and orientation for the right and left sides in respect to the patient’s own body, as well as that of other persons, often with special reference to the hands and fingers. These disorders are commonly combined with an isolated disability for writing-dysor agraphiaand an isolated disability for calculation -dysor acalculia-of differing severity and definite character, both types of disorder varying in significant respects from the aphasic, apraxic, and spatial-agnostic types. The disturbances tend to aDpear in varying degrees of development. All these symptoms group themselves phenomenologically and psychologically into a well circumscribed syndrome. Investigations in a large number of cases of this type have so far failed to reveal any evidence of psychic or intellectual disorder, aphasia, apraxia, or other manifestations of agnosis (particularly with regard to outer space and objects therein) or of motor or sensow changes to which the symptom-complex of finger agnosia and its accompanying individual features
Push and Rotate: a Complete Multi-agent Pathfinding Algorithm

Multi-agent Pathfinding is a relevant problem in a wide range of domains, for example in robotics and video games research. Formally, the problem considers a graph consisting of vertices and edges, and a set of agents occupying vertices. An agent can only move to an unoccupied, neighbouring vertex, and the problem of finding the minimal sequence of moves to transfer each agent from its start location to its destination is an NP-hard problem. We present Push and Rotate, a new algorithm that is complete for Multi-agent Pathfinding problems in which there are at least two empty vertices. Push and Rotate first divides the graph into subgraphs within which it is possible for agents to reach any position of the subgraph, and then uses the simple push, swap, and rotate operations to find a solution; a post-processing algorithm is also presented that eliminates redundant moves. Push and Rotate can be seen as extending Luna and Bekris's Push and Swap algorithm, which we showed to be incomplete in a previous publication. In our experiments we compare our approach with the Push and Swap, MAPP, and Bibox algorithms. The latter algorithm is restricted to a smaller class of instances as it requires biconnected graphs, but can nevertheless be considered state of the art due to its strong performance. Our experiments show that Push and Swap suffers from incompleteness, MAPP is generally not competitive with Push and Rotate, and Bibox is better than Push and Rotate on randomly generated biconnected instances, while Push and Rotate performs better on grids.
Estimating Gene Expression and Codon-Specific Translational Efficiencies, Mutation Biases, and Selection Coefficients from Genomic Data Alone‡

Extracting biologically meaningful information from the continuing flood of genomic data is a major challenge in the life sciences. Codon usage bias (CUB) is a general feature of most genomes and is thought to reflect the effects of both natural selection for efficient translation and mutation bias. Here we present a mechanistically interpretable, Bayesian model (ribosome overhead costs Stochastic Evolutionary Model of Protein Production Rate [ROC SEMPPR]) to extract meaningful information from patterns of CUB within a genome. ROC SEMPPR is grounded in population genetics and allows us to separate the contributions of mutational biases and natural selection against translational inefficiency on a gene-by-gene and codon-by-codon basis. Until now, the primary disadvantage of similar approaches was the need for genome scale measurements of gene expression. Here, we demonstrate that it is possible to both extract accurate estimates of codon-specific mutation biases and translational efficiencies while simultaneously generating accurate estimates of gene expression, rather than requiring such information. We demonstrate the utility of ROC SEMPPR using the Saccharomyces cerevisiae S288c genome. When we compare our model fits with previous approaches we observe an exceptionally high agreement between estimates of both codon-specific parameters and gene expression levels (ρ>0.99 in all cases). We also observe strong agreement between our parameter estimates and those derived from alternative data sets. For example, our estimates of mutation bias and those from mutational accumulation experiments are highly correlated (ρ=0.95). Our estimates of codon-specific translational inefficiencies and tRNA copy number-based estimates of ribosome pausing time (ρ=0.64), and mRNA and ribosome profiling footprint-based estimates of gene expression (ρ=0.53−0.74) are also highly correlated, thus supporting the hypothesis that selection against translational inefficiency is an important force driving the evolution of CUB. Surprisingly, we find that for particular amino acids, codon usage in highly expressed genes can still be largely driven by mutation bias and that failing to take mutation bias into account can lead to the misidentification of an amino acid’s “optimal” codon. In conclusion, our method demonstrates that an enormous amount of biologically important information is encoded within genome scale patterns of codon usage, accessing this information does not require gene expression measurements, but instead carefully formulated biologically interpretable models.
DNA-linked Inhibitor Antibody Assay (DIANA) for sensitive and selective enzyme detection and inhibitor screening

Human diseases are often diagnosed by determining levels of relevant enzymes and treated by enzyme inhibitors. We describe an assay suitable for both ultrasensitive enzyme quantification and quantitative inhibitor screening with unpurified enzymes. In the DNA-linked Inhibitor ANtibody Assay (DIANA), the target enzyme is captured by an immobilized antibody, probed with a small-molecule inhibitor attached to a reporter DNA and detected by quantitative PCR. We validate the approach using the putative cancer markers prostate-specific membrane antigen and carbonic anhydrase IX. We show that DIANA has a linear range of up to six logs and it selectively detects zeptomoles of targets in complex biological samples. DIANA's wide dynamic range permits determination of target enzyme inhibition constants using a single inhibitor concentration. DIANA also enables quantitative screening of small-molecule enzyme inhibitors using microliters of human blood serum containing picograms of target enzyme. DIANA's performance characteristics make it a superior tool for disease detection and drug discovery.
Bond performance of GFRP and deformed steel hybrid bar with sand coating to concrete

In this study, we experimentally investigated the bond performance of a glass fiber-reinforced polymer hybrid bar with a core section comprising a deformed steel bar and a sand coating. The glass fiber-reinforced polymer and deformed steel hybrid bar (glass fiber-reinforced polymer hybrid bar) can contribute to longer durability and better serviceability of reinforced concrete members because of the increased modulus of elasticity provided by the deformed steel bar. Uniaxial tensile tests in compliance with ASTM D 3916 showed that the modulus of elasticity of the glass fiber-reinforced polymer hybrid bar was enhanced up to three times. For the bond test, a total of 30 specimens with various sand-coating and surface design parameters such as the size of the sand particles (0.6 mm and 0.3 mm), sand-coating type (partially or completely), number of strands of fiber ribs (6 and 10), and pitch space (11.4 mm to 29.1 mm) of the fiber ribs were tested. The completely sand-coated glass fiber-reinforced polymer hybrid bar exhibited a higher bond strength (90.5%) than the deformed steel bar and a reasonable mode of failure in concrete splitting. A modification parameter to the Eligehausen, Popov, and Bertero (BPE) model is suggested based on the representative experimental tests. The bond stress–slip behavior suggested by the modified BPE model in this study was in reasonable agreement with the experimental results.
Transfer Entropy and Directed Information in Gaussian diffusion processes

Transfer Entropy and Directed Information are information-theoretic measures of the directional dependency between stochastic processes. Following the definitions of Schreiber and Massey in discrete time, we define and evaluate these measures for the components of multidimensional Gaussian diffusion processes. When the components are jointly Markov, the Transfer Entropy and Directed Information are both measures of influence according to a simple physical principle. More generally, the effect of other components has to be accounted for, and this can be achieved in more than one way. We propose two definitions, one of which preserves the properties of influence of the jointly Markov case. The Transfer Entropy and Directed Information are expressed in terms of the solutions of matrix Riccati equations, and so are easy to compute. The definition of continuous-time Directed Information we propose differs from that previously appearing in the literature. We argue that the latter is not strictly directional.
Phase I Dose-Escalation Study of Proton Beam Therapy for Inoperable Hepatocellular Carcinoma

Purpose The purpose of this study is to determine the optimal dose of proton beam therapy (PBT) in hepatocellular carcinoma (HCC) patients. Materials and Methods Inoperable HCC patients who had naïve, recurrent, or residual tumor to treatment were considered eligible for PBT. Patients received PBT with 60 GyE in 20 fractions (dose level 1; equivalent dose in 2 Gy fractions [EQD2], 65 GyE10); 66 GyE in 22 fractions (dose level 2; EQD2, 71.5 GyE10); or 72 GyE in 24 fractions (dose level 3; EQD2, 78 GyE10). Dose-limiting toxicity was determined by grade ≥ 3 acute toxicity. Results Twenty-seven patients were enrolled; eight, seven, and 12 patients were treated with dose levels 1, 2, and 3, respectively. Overall, treatment was well tolerated, with no dose-limiting toxicities. The complete response (CR) rates of primary tumors after PBT for dose levels 1, 2, and 3 were 62.5% (5/8), 57.1% (4/7), and 100% (12/12), respectively (p=0.039). The 3-and 5-year local progression-free survival (LPFS) rates among 26 patients, excluding one patient who underwent liver transplantation after PBT due to its probable significant effect on disease control, were 79.9% and 63.9%, respectively, and the 3-and 5-year overall survival rates were 56.4% and 42.3%, respectively. The 3-year LPFS rate was significantly higher in patients who achieved CR than in those who did not (90% vs. 40%, p=0.003). Conclusion PBT is safe and effective and an EQD2 ≥ 78 GyE10 should be delivered for achievement of local tumor control.
Analysis of 1008 Consecutive Patients Aged 15 to 49 With First-Ever Ischemic Stroke: The Helsinki Young Stroke Registry

Background and Purpose— To analyze trends in occurrence, risk factors, etiology, and neuroimaging features of ischemic stroke in young adults in a large cohort. Methods— We evaluated all 1008 consecutive ischemic stroke patients aged 15 to 49 admitted to Helsinki University Central Hospital, 1994 to 2007. Etiology was classified by Trial of Org 10172 in Acute Stroke Treatment criteria. Comparisons were done between groups stratified by gender and age. Results— Estimated annual occurrence was 10.8/100 000 (range 8.4 to 13.0), increasing exponentially with aging. Of our 628 male and 380 female (ratio 1.7:1) patients, females were preponderant among those <30, whereas male dominance rapidly increased around age of 44. The most frequent risk factors were dyslipidemia (60%), smoking (44%), and hypertension (39%). Males and patients >44 clearly had more risk factors. Cardioembolism (20%) and cervicocerebral artery dissection (15%) were the most frequent etiologic subgroups. Proportions of large-artery atherosclerosis (8%) and small-vessel disease (14%) began to enlarge at age 35, whereas frequency of undetermined etiology (33%) decreased along aging. Posterior circulation infarcts were more common among patients <45 years of age. Left hemisphere infarcts were more frequent in general. There were 235 (23%) patients with multiple and 126 (13%) with silent infarcts, and 55 (5%) patients had leukoaraiosis. Conclusions— The frequency of ischemic stroke increases sharply at age 40. Etiology and risk factors start resembling those seen in the elderly in early midlife but causes defined in younger patients still are frequent in those aged 45 to 49. Subclinical infarcts were surprisingly common in the young.
Toxoplasmosis – A Global Threat. Correlation of Latent Toxoplasmosis with Specific Disease Burden in a Set of 88 Countries

Background Toxoplasmosis is becoming a global health hazard as it infects 30–50% of the world human population. Clinically, the life-long presence of the parasite in tissues of a majority of infected individuals is usually considered asymptomatic. However, a number of studies show that this ‘asymptomatic infection’ may also lead to development of other human pathologies. Aims of the Study The purpose of the study was to collect available geoepidemiological data on seroprevalence of toxoplasmosis and search for its relationship with mortality and disability rates in different countries. Methods and Findings Prevalence data published between 1995–2008 for women in child-bearing age were collected for 88 countries (29 European). The association between prevalence of toxoplasmosis and specific disease burden estimated with age-standardized Disability Adjusted Life Year (DALY) or with mortality, was calculated using General Linear Method with Gross Domestic Product per capita (GDP), geolatitude and humidity as covariates, and also using nonparametric partial Kendall correlation test with GDP as a covariate. The prevalence of toxoplasmosis correlated with specific disease burden in particular countries explaining 23% of variability in disease burden in Europe. The analyses revealed that for example, DALY of 23 of 128 analyzed diseases and disease categories on the WHO list showed correlations (18 positive, 5 negative) with prevalence of toxoplasmosis and another 12 diseases showed positive trends (p<0.1). For several obtained significant correlations between the seroprevalence of toxoplasmosis and specific diseases/clinical entities, possible pathophysiological, biochemical and molecular explanations are presented. Conclusions The seroprevalence of toxoplasmosis correlated with various disease burden. Statistical associations does not necessarily mean causality. The precautionary principle suggests however that possible role of toxoplasmosis as a triggering factor responsible for development of several clinical entities deserves much more attention and financial support both in everyday medical practice and future clinical research.
Surgical Outcome of One-stage and Two-stage Flexor Tendon Grafting in Children

Background Flexor tendon grafting represents the most common modality for secondary restoration of flexor tendon function. Tendon grafting is either performed in 1 or 2 stages. This study attempts to evaluate the clinical outcome of 1-stage and 2-stage grafting in children. Methods A retrospective review was performed identifying 20 children treated for secondary rupture of the flexor digitorum longus by means of a tendon graft. There were 17 boys and 3 girls with a mean age of 10.8 years (range: 3 to 15) at the time of surgery. The preoperative condition of each operated finger was graded by the digital damage classification recommended by Merle and Dautel. Functional status was obtained throughout follow-up using the Strickland classification. Results There were 10 children in grade 1, 6 grade 2, and 4 grade 3 according to Merle and Dautel classification. The delay between the initial trauma or primary procedure and the secondary surgical procedure averaged 7.5 months for 1-stage grafting and 9 months for 2-stage grafting (range: 1 mo to 2 y). The median Strickland index was 70 (range: 55 to 114) for 1-stage grafting and 66 (range 0 to 103) for 2-stage grafting, which was not statistically different (P=0.1). Conclusions The functional outcome seems to depend on the initial severity index. One-stage grafting is a relevant procedure when pulleys are intact and the range of motion is complete. When neurovascular bundles are injured a 1-stage grafting should not be tempted. Satisfactory results are expected with 2-stage grafting providing the principles of this procedure are carefully adhered to. Level of evidence Level 4.
Dense graphs are antimagic

An antimagic labeling of graph a with m edges and n vertices is a bijection from the set of edges to the integers 1,…,m such that all n vertex sums are pairwise distinct, where a vertex sum is the sum of labels of all edges incident with the same vertex. A graph is called antimagic if it has an antimagic labeling. A conjecture of Ringel (see 4 ) states that every connected graph, but K2, is antimagic. Our main result validates this conjecture for graphs having minimum degree Ω (log n). The proof combines probabilistic arguments with simple tools from analytic number theory and combinatorial techniques. We also prove that complete partite graphs (but K2) and graphs with maximum degree at least n – 2 are antimagic. © 2004 Wiley Periodicals, Inc. J Graph Theory 47: 297–309, 2004
Digital self triggered robust control of nonlinear systems

In this paper we develop novel results on self triggering control of nonlinear systems, subject to perturbations and actuation delays. First, considering an unperturbed nonlinear system with bounded actuation delays, we provide conditions that guarantee the existence of a self triggering control strategy stabilizing the closed-loop system. Then, considering parameter uncertainties, disturbances, and bounded actuation delays, we provide conditions guaranteeing the existence of a self triggering strategy, that keeps the state arbitrarily close to the equilibrium point. In both cases, we provide a methodology for the computation of the next execution time. We show on an example the relevant benefits obtained with this approach, in terms of energy consumption, with respect to control algorithms based on a constant sampling, with a sensible reduction of the average sampling time.
Matrix Metalloproteinase (MMP)-9 in Cancer-Associated Fibroblasts (CAFs) Is Suppressed by Omega-3 Polyunsaturated Fatty Acids In Vitro and In Vivo

Cancer associated fibroblasts (CAFs) are responsible for tumor growth, angiogenesis, invasion, and metastasis. Matrix metalloproteinase (MMP)-9 secreted from cancer stroma populated by CAFs is a prerequisite for cancer angiogenesis and metastasis. Omega-3 polyunsaturated fatty acids (omega-3 PUFA) have been reported to have anti-tumor effects on diverse types of malignancies. Fat-1 mice, which can convert omega-6 to omega-3 PUFA independent of diet, are useful to investigate the functions of endogenous omega-3 PUFA. To examine the effect of omega-3 PUFA on tumorigenesis, TC-1 cells, a murine epithelial cell line immortalized by human papillomavirus (HPV) oncogenes, were injected subcutaneously into fat-1 or wild type mice. Tumor growth and angiogenesis of the TC-1 tumor were significantly suppressed in fat-1 compared to wild type mice. cDNA microarray of the tumors derived from fat-1 and wild type mice revealed that MMP-9 is downregulated in fat-1 mice. Immunohistochemical study demonstrated immunoreactivity for MMP-9 in the tumor stromal fibroblasts was diffusely positive in wild type whereas focal in fat-1 mice. MMP-9 was expressed in primary cultured fibroblasts isolated from fat-1 and wild type mice but was not expressed in TC-1 cells. Co-culture of fibroblasts with TC-1 cells enhanced the expression and the proteinase activity of MMP-9, although the protease activity of MMP-9 in fat-1-derived fibroblasts was lower than that in wild type fibroblasts. Our data suggests that omega-3 PUFAs suppress MMP-9 induction and tumor angiogenesis. These findings may provide insight into mechanisms by which omega-3 PUFAs exert anti-tumor effects by modulating tumor microenvironment.