Miracle-dz/UniFAR-FTUs huggingface dataset:
Teams of pushdown automata

We introduce team pushdown automata (PDAs) as a theoretical framework capable of modelling various communication and cooperation strategies in complex, distributed systems. Team PDAs are obtained by augmenting distributed PDAs with the notion of team cooperation or, alternatively, by augmenting team automata with pushdown memory. In a team PDA, several PDAs work as a team on the input word placed on a common one-way input tape. At any moment in time one team of PDAs, each with the same symbol on top of its stack, is active: each PDA in the active team replaces the topmost symbol of its stack and changes state, while the current input symbol is read from the input tape by a common reading head. The teams are formed according to the team cooperation strategy of the team PDA and may vary from one moment to the other. Based on the notion of competence, we introduce a variety of team cooperation strategies. If all stacks are empty when the input word has been completely read, then this word is part of the language accepted by the team PDA. Here we focus on the accepting capacity of team PDA. †E-mail: csuhaj@sztaki.hu ‡E-mail: mitrana@funinf.cs. unibuc.ro
Language comprehension profiles in Alzheimer's disease, multi-infarct dementia, and frontotemporal degeneration

We assessed language functioning in 116 age-, education-, and severity-matched patients with the clinical diagnosis of Alzheimer's disease (AD), multi-infarct dementia (MID) due to small-vessel ischemic disease, or a frontotemporal form of degeneration (FD). Assessments of comprehension revealed that patients with AD are significantly impaired in their judgments of single word and picture meaning, whereas patients with FD had sentence comprehension difficulty due to impaired processing of grammatical phrase structure. Patients with MID did not differ from control subjects in their comprehension performance. Traditional aphasiologic measures did not distinguish between AD, MID, and FD. Selective patterns of comprehension difficulty in patients with different forms of dementia emphasize that language deficits cannot be explained entirely by the compromised memory associated with a progressive neurodegenerative illness. NEUROLOGY 1996;47: 183-189
IL-2 But Not Cytolytic Activity Cytolytic T Cells and Responsiveness to + CD8CD137 Promotes Both Helper Function for Signaling Through NK Cell-Associated

NK cells possess both effector and regulatory activities that may be important during the antitumor immune response. In fact, the generation of antitumor immunity by the administration of an agonistic mAb against CD137 is NK cell-dependent. In this study, we report that NK cells could be induced by IL-2 and IL-15 to express CD137 and ligation of CD137-stimulated NK cell proliferation and IFN- (cid:2) secretion, but not their cytolytic activity. Importantly, CD137-stimulated NK cells promoted the expansion of activated T cells in vitro, demonstrating immunoregulatory or “helper” activity for CD8 (cid:1) CTL. Furthermore, tumor-speciﬁc CTL activity against P815 tumor Ags was abrogated following anti-CD137 treatment in NK-depleted mice. We further demonstrate that CD137-stimulated helper NK cells expressed the high-afﬁnity IL-2R and were hyperresponsive to IL-2. Taken together with previous ﬁndings that CD137 is a critical receptor for costimulation of T cells, our ﬁndings suggest that CD137 is a stimulatory receptor for NK cells involved in the crosstalk between innate and adaptive immunity. The Journal of Immunology, 2002, 169: 4230–4236.
Net primary production of terrestrial ecosystems in China and its equilibrium response to changes in climate and atmospheric CO₂ concentration

We used the Terrestrial Ecosystem Model (TEM, version 4.0) to estimate net primary production (NPP) in China for contemporary climate and NPP responses to elevated CO2 and climate changes projected by three atmospheric general circulation models (GCMs): Goddard Institute for Space Studies (GISS), Geophysical Fluid Dynamic Laboratory (GFDL) and Oregon State University (OSU). For contemporary climate at 312.5 ppmv CO2, TEM estimates that China has an annual NPP of 3,653 TgC yr (10 gC yr). Temperate broadleaf evergreen forest is the most productive biome and accounts for the largest portion of annual NPP in China. The spatial pattern of NPP is closely correlated to the spatial distributions of precipitation and temperature. Annual NPP of China is sensitive to changes in CO2 and climate. At the continental scale, annual NPP of China increases by 6.0% (219 TgC yr) for elevated CO2 only (519 ppmv CO2). For climate change with no change in CO2, the response of annual NPP ranges from a decrease of 1.5% (54.8 TgC yr) for the GISS climate to an increase of 8.4% (306.9 TgC yr) for the GFDL-q climate. For climate change at 519 ppmv CO2, annual NPP of China increases substantially, ranging from 18.7% (683 TgC yr) for the GISS climate to 23.3% (851 TgC yr) for the GFDL-q climate. Spatially, the responses of annual NPP to changes in climate and CO2 vary considerably within a GCM climate. Differences among the three GCM climates used in the study cause large differences in the geographical distribution of NPP responses to projected climate changes. The interaction between elevated CO2 and climate change plays an important role in the overall response of NPP to climate change at 519 ppmv CO2. Submitted to: Acta Phytoecologica Sinica (published in China) Author responsible for correspondence: Dr. Xiangming Xiao, The Ecosystems Center, Marine Biological Laboratory, Woods Hole, MA 02543, Tel: (508)289-7498, Fax: (508)457-1548, Email: xiao@lupine.mbl. edu
Resistance of Yersinia pestis to Complement-Dependent Killing Is Mediated by the Ail Outer Membrane Protein

ABSTRACT Yersinia pestis, the causative agent of plague, must survive in blood in order to cause disease and to be transmitted from host to host by fleas. Members of the Ail/Lom family of outer membrane proteins provide protection from complement-dependent killing for a number of pathogenic bacteria. The Y. pestis KIM genome is predicted to encode four Ail/Lom family proteins. Y. pestis mutants specifically deficient in expression of each of these proteins were constructed using lambda Red-mediated recombination. The Ail outer membrane protein was essential for Y. pestis to resist complement-mediated killing at 26 and 37°C. Ail was expressed at high levels at both 26 and 37°C, but not at 6°C. Expression of Ail in Escherichia coli provided protection from the bactericidal activity of complement. High-level expression of the three other Y. pestis Ail/Lom family proteins (the y1682, y2034, and y2446 proteins) provided no protection against complement-mediated bacterial killing. A Y. pestis ail deletion mutant was rapidly killed by sera obtained from all mammals tested except mouse serum. The role of Ail in infection of mice, Caenorhabditis elegans, and fleas was investigated.
Very long-term ECG monitoring patch with improved functionality and wearability

Heart activity monitoring is an important task for prevention and treatment of cardiovascular diseases. However, development of long-term, wearable electrodes remains an open issue. In fact, adhesion ability and energy consumption while preserving aesthetics is one of the major concerns to implement a minimally invasive monitoring system that measures and transmits electrocardiographic signals (ECG) during long-term periods of time. Based on the concepts of functionality, wearability, and resources, we develop a new long-term ECG monitoring system under the wear-and-forget principle. We also propose a system model of the electrode-skin interface that performs real-time measurements with a minimally invasive effect when compared with another competitive and implantable systems. As a result, testing of designed prototype shows that the developed very long-term ECG monitoring patch improves energy consumption and adhesion time up to 40 days.
Classification and generation of schedules for VLIW processors

Exact methods for optimal instruction scheduling are gaining importance. They differ, however, considerably in the assumed processor model and in the space of schedules searched for an optimal solution. We identify and analyze different classes of schedules for VLIW processors. The classes are induced by various common techniques for generating or enumerating them, such as integer linear programming or list scheduling with backtracking. In particular, we study the relationship between VLIW schedules and their equivalent linearized forms (which may be used, e.g., with superscalar processors), and we identify classes of VLIW schedules that can be created from a linearized form using VLIW compaction methods that are just the static equivalents of dynamic instruction dispatch algorithms of in‐order and out‐of‐order issue superscalar processors. For example, we study the class of greedy schedules and show that, if all instructions have multiblock reservation tables, it is safe for time optimization to consider greedy schedules only. We also show that, in certain situations, certain schedules generally cannot be constructed by incremental scheduling algorithms that are based on topological sorting of the data dependence graph. We summarize our findings as a hierarchy of classes of VLIW schedules. These results can sharpen the interpretation of the term ‘optimality’ used with various methods for optimal VLIW scheduling, and may help to identify classes that can be safely ignored when searching for an optimal schedule. Copyright © 2007 John Wiley & Sons, Ltd.
Comparative Study of Mucoadhesive Vaginal Film and Tablet of Curcumin

Vaginal candidiasis is a common condition and up to 75% of women suffer at least one episode of this infection during their life time. Candida albicans is the most important cause of this, accounting for over 80% of the infections.Curcumin is a phytochemical, a component of folklore medicine since ages. Ithas been investigated as anti-inflammatory, anticancer, antimicrobial, and antifungal.Mucoadhesion has been propose for a variety of local as well as systemic purposes. Systems like tablets, films, gels, liquids and multiparticulates have been employed successfully. The objective of the present work was to formulate mucoadhesive vaginal film and tablet of Curcumin for the treatment of vaginal candidiasis is, and compare their performance. Film was cast by solvent evaporation method while tablet was prepared by direct compression. Both formulations were designed by using Xanthan gum and HPMC K15M. Evaluation and comparison was accomplished through parameters like mucoadhesion, drug release and zone of inhibition. Mucoadhesive strength of film was better at0.37mJ. Drug release found was 90-95% for film while 80-85% for tablet in 12 h.Antimicrobial study of film showed better performance than tablet against Candida albicans. The study reflected mucoadhesive curcumin films would be a better choice than tablets for vaginal candidiasis.
Interaction Trap/Two‐Hybrid System to Identify Interacting Proteins

The parameters and experimental conditions for this important system are constantly undergoing improvement. This newest version includes expanded tables describing interaction trap components and additional libraries compatible with the interaction trap system. It also features a new protocol on performing a hunt by interaction mating. Some of the commercial vendors selling yeast two‐hybrid reagents recommend using interaction mating to perform a hunt, so this procedure should be of great interest.
Intensive dietary counseling does not affect oncologic outcome.

I read with interest the article by Ravasco et al (1) in the December issue of the Journal, and I was impressed by their Figure 1, which showed the survival of the 3 arms of their study and especially that of group 1 patients (intensive counseling) who had a 5-y survival of ;100%. I am not aware of any oncologic study involving patients with an advanced colorectal cancer—and hence undergoing a preoperative or postoperative oncologic treatment or a palliative one, as reported in the original article (2)—who had such a survival rate, which perhaps might be observed only in early-stage (Dukes’ A) cancer patients. I think that differences in survival are better explained by an inhomogeneous distribution of patients with different severity of disease within the 3 arms, and arm 1 included the most favorable cases. This unfortunately represents an important bias, which invalidates the conclusions of the authors.
Vasopressin Inhibits Glutamate Release via Two Distinct Modes in the Brainstem

The hypothalamus coordinates autonomic responses in part through arginine vasopressin (AVP) released in medial nucleus tractus solitarius (NTS). However, the mechanisms and sites of AVP action within NTS pathways are uncertain. In brainstem slices, we activated solitary tract (ST) primary afferents to release glutamate and tested whether AVP modulated synaptic transmission to second-order neurons. NTS neurons were classified as second order by ST synaptic characteristics or the presence of anterograde tracers from peripheral baroreceptor afferents. Stimulus recruitment curves indicated ST-EPSCs on individual neurons were evoked by stimulation of single ST axons. Variance–mean (V–M) analysis of ST-EPSCs in individual neurons revealed uniformly high release probability (p ∼ 0.9) from an average of 19 release sites (N) and a quantal size (q) of 34.0 ± 4.7 pA. In 26 of 49 neurons, AVP inhibited afferent synaptic transmission. In most neurons, AVP reduced ST-EPSC amplitudes (n = 20) by decreasing p to 0.65, whereas q, N, and conduction times were unaffected. The V1a antagonist SR49059 alone decreased ST-EPSC V and increased M, suggesting tonic AVP actions, and blocked exogenous AVP action (n = 4). In other neurons with identical ST release properties, AVP induced synaptic failures and increased conduction time without altering the V–M relationship of successful ST-EPSCs (n = 6). Interestingly, frequency-depressed ST-EPSCs were not affected by AVP. AVP failed to alter holding or voltage-dependent potassium currents. Thus, AVP regulates NTS neurons by two distinct novel and state-dependent mechanisms: one, an analog, graded presynaptic inhibition of terminal glutamate release and the other, a binary, extraterminal block of conducted excitation.
Rejection Factors of Pull Requests Filed by Core Team Developers in Software Projects with High Acceptance Rates

When developers want to contribute to an opensource project, they fork the repository, make changes, and send a pull request to the core team to incorporate these changes back into the repository. However, some projects enforce this collaboration model even for changes made by core team developers. This potentially enhances the quality of the repository by adding an inspection step before accepting a contribution into the repository. In this context, though less frequently, the contributions may be rejected. The understanding of the factors that lead to the rejection of these internal contributions is crucial for the improvement of the ways core developers collaborate, having a direct impact on the team productivity. In this work we extract association rules from pull request data stored in software repositories in order to find factors that have influence over the decision of rejecting contributions made by core developers. In addition, we present a qualitative analysis of some cases, helping to understand the patterns that arose from the association rules. The results indicate that some key factors increase the changes of having internal contributions rejected: (i) the inexperience with pull requests, (ii) the complexity of contributions, as well as the locality of the artifacts that have been modified, and (iii) the contribution policy of the projects.
Stabilizing and robustifying the learning mechanisms of artificial neural networks in control engineering applications

This paper discusses the stabilizability of artificial neural networks trained by utilizing the gradient information. The method proposed constructs a dynamic model of the conventional update mechanism and derives the stabilizing values of the learning rate. The stability in this context corresponds to the convergence in adjustable parameters of the neural network structure. It is shown that the selection of the learning rate as imposed by the proposed algorithm results in stable training in the sense of Lyapunov. Furthermore, the algorithm devised filters out the high frequency dynamics of the gradient descent method. The excitation of this dynamics typically occurs in the presence of noise and abruptly changing the parameters of the mapping being learned. This adversely influences the learning performance that can be attained during a training cycle. A natural consequence following this excitation is divergence in parameter space. The method analyzed in this paper integrates the gradient descent technique with variable structure systems methodology, which is well known for its robustness to environmental disturbances. In the simulations, control of a three degrees of freedom anthropoid robot is chosen for the evaluation of the performance. For this purpose, a feedforward neural network structure is utilized as the controller. Highly nonlinear dynamics of the plant, existence of a considerable amount of observation noise, and the adverse effects of gravitational forces constitute the difficulties to be alleviated by the neurocontroller trained with the proposed method. In order to come up with a fair comparison, the results obtained with the pure gradient descent technique with the same initial conditions are also presented and discussed. © 2000 John Wiley & Sons, Inc.
Mechanism of 4-aminopyridine action on voltage-gated potassium channels in lymphocytes

The mechanism by which 4-aminopyridine (4-AP) blocks the delayed rectifier type potassium (K+) channels present on lipopolysaccharide- activated murine B lymphocytes was investigated using whole-cell and single channel patch-clamp recordings. 4-AP (1 microM-5 mM) was superfused for 3-4 min before applying depolarizing pulses to activate the channel. During the first pulse after application of 4-AP above 50 microM, the current inactivated faster, as compared with the control, but its peak was only reduced at high concentrations of 4-AP (Kd = 3.1 mM). During subsequent pulses, the peak current was decreased (Kd = 120 microM), but the inactivation rate was slower than in the control, a feature that could be explained by a slow unblocking process. After washing out the drug, the current elicited by the first voltage step was still markedly reduced, as compared with the control one, and displayed very slow activation and inactivation kinetics; this suggests that the K+ channels move from a blocked to an unblocked state slowly during the depolarizing pulse. These results show that 4-AP blocks K+ channels in their open state and that the drug remains trapped in the channel once it is closed. On the basis of the analysis of the current kinetics during unblocking, we suggest that two pathways lead from the blocked to the unblocked states. Computer simulations were used to investigate the mechanism of action of 4-AP. The simulations suggest that 4-AP must bind to both an open and a nonconducting state of the channel. It is postulated that the latter is either the inactivated channel or a site on closed channels only accessible to the drug once the cell has been depolarized. Using inside- and outside-out patch recordings, we found that 4-AP only blocks channels from the intracellular side of the membrane and acts by reducing the mean burst time. 4-AP is a weak base (pK = 9), and thus exists in ionized or nonionized form. Since the Kd of channel block depends on both internal and external pH, we suggest that 4-AP crosses the membrane in its nonionized form and acts from inside the cell in its ionized form.
Immunogenicity and Protective Efficacy of a Dual Subunit Vaccine Against Respiratory Syncytial Virus and Influenza Virus

Respiratory syncytial virus (RSV) and influenza virus are the most significant pathogens causing respiratory tract diseases. Composite vaccines are useful in reducing the number of vaccination and confer protection against multiple infectious agents. In this study, we generated fusion of RSV G protein core fragment (amino acid residues 131 to 230) and influenza HA1 globular head domain (amino acid residues 62 to 284) as a dual vaccine candidate. This fusion protein, Gcf-HA1, was bacterially expressed, purified by metal resin affinity chromatography, and refolded in PBS. BALB/c mice were intranasally immunized with Gcf-HA1 in combination with a mucosal adjuvant, cholera toxin (CT). Both serum IgG and mucosal IgA responses specific to Gcf and HA1 were significantly increased in Gcf-HA1/CT-vaccinated mice. To determine the protective efficacy of Gcf-HA1/CT vaccine, immunized mice were challenged with RSV (A2 strain) or influenza virus (A/PR/8/34). Neither detectable viral replication nor pathology was observed in the lungs of the immune mice. These results demonstrate that immunity induced by intranasal Gcf-HA1/CT immunization confers complete protection against both RSV and homologous influenza virus infection, suggesting our Gcf-HA1 vaccine candidate could be further developed as a dual subunit vaccine against RSV and influenza virus.
Geometrical phases and symmetries in dissipative systems.

A geometrical phase is constructed for dissipative dynamical systems possessing continuous symmetries. It emerges as the natural analog of the holonomy associated with the adiabatic variation of parameters in quantum-mechanical and classical Hamiltonian systems. In continuous media, the physical manifestation of this phase is a spatial shift of a wave pattern, typically a translation or rotation. An illustration associated with pattern formation in fluids is provided
Activation of Rubisco regulates photosynthesis at high temperature and CO2.

The enzyme Rubisco, short for ribulose-1,5-bisphosphate carboxylase/oxygenase, is the enzyme that incorporates CO2 into plants during photosynthesis. As it constitutes about 30% of the total protein in a plant leaf, Rubisco is probably the most abundant protein on earth and a major sink for plant nitrogen. Rubisco is widely accepted as the ultimate rate-limiting step in photosynthetic carbon fixation. Atmospheric oxygen competes with CO2 as a substrate for Rubisco, giving rise to photorespiration. When first purified, the enzyme appeared to have a poor affinity for CO2 [Km (CO2)] of 450 μM (1), whereas air in equilibrium with water, 25°C, is about 10 μM. Later, Lorimer et al. (2) showed that the active site of Rubisco must first be carbamylated by an activator CO2, separate from the substrate CO2, and must bind Mg2+ before binding the five-carbon substrate, ribulose-1,5-bisphosphate (RuBP). Indeed, on addition of RuBP, the measured Km(CO2) approached the concentrations of dissolved CO2 in water; however, the rate of the reaction was sustained for only 5 minutes and then declined rapidly. This decline was shown to be caused by the tight binding of RuBP to Rubisco that had lost the activator CO …