Miracle-dz/UniFAR-FTUs huggingface dataset:
Large-Scale 13C Flux Profiling Reveals Conservation of the Entner-Doudoroff Pathway as a Glycolytic Strategy among Marine Bacteria That Use Glucose

ABSTRACT Marine bacteria form one of the largest living surfaces on Earth, and their metabolic activity is of fundamental importance for global nutrient cycling. Here, we explored the largely unknown intracellular pathways in 25 microbes representing different classes of marine bacteria that use glucose: Alphaproteobacteria, Gammaproteobacteria, and Flavobacteriia of the Bacteriodetes phylum. We used 13C isotope experiments to infer metabolic fluxes through their carbon core pathways. Notably, 90% of all strains studied use the Entner-Doudoroff (ED) pathway for glucose catabolism, whereas only 10% rely on the Embden-Meyerhof-Parnas (EMP) pathway. This result differed dramatically from the terrestrial model strains studied, which preferentially used the EMP pathway yielding high levels of ATP. Strains using the ED pathway exhibited a more robust resistance against the oxidative stress typically found in this environment. An important feature contributing to the preferential use of the ED pathway in the oceans could therefore be enhanced supply of NADPH through this pathway. The marine bacteria studied did not specifically rely on a distinct anaplerotic route, but the carboxylation of phosphoenolpyruvate (PEP) or pyruvate for fueling of the tricarboxylic acid (TCA) cycle was evenly distributed. The marine isolates studied belong to clades that dominate the uptake of glucose, a major carbon source for bacteria in seawater. Therefore, the ED pathway may play a significant role in the cycling of mono- and polysaccharides by bacterial communities in marine ecosystems.
Observational Study of the Relation between Parkinson's Disease and Sleep Apnea.

BACKGROUND Parkinson's disease is characterized by numerous non-motor symptoms, including sleep disorders. Sleep apnea has been reported in a substantial proportion of patients with Parkinson's disease, but it is unclear whether it has significant consequences for the quality of life of those affected or whether it is associated with other manifestations of the disease. OBJECTIVE To verify whether sleep apnea is associated with more severe motor and non-motor clinical features in Parkinson's disease. METHODS Parkinson's disease patients underwent polysomnography to diagnose the presence of sleep apnea (apnea-hypopnoea index >10). Participants also underwent an extensive assessment, blinded to sleep apnea status, to determine disease severity, quantitative motor indices, motor subtypes, treatment complications, and sleep, autonomic, psychiatric, and sensory dysfunctions. Cognitive status was also determined with a complete neuropsychological assessment. Results were assessed using regression analysis adjusted for age, sex, and disease duration. RESULTS Of 92 patients examined, 19 had sleep apnea (21%) and 73 did not. We found no significant differences in motor and non-motor symptoms or signs between apneic and non-apneic Parkinson's disease patients. The use of different apnea-hypopnoea index cut-offs (>5 and >15) produced similar results. CONCLUSIONS Our results show that sleep apnea is not associated with more severe motor or non-motor manifestations in Parkinson's disease. More studies including control groups are needed to confirm the implications of those results.
Effect of Trail Bifurcation Asymmetry and Pheromone Presence or Absence on Trail Choice by Lasius niger Ants

During foraging, ant workers are known to make use of multiple information sources, such as private information (personal memory) and social information (trail pheromones). Environmental effects on foraging, and how these interact with other information sources, have, however, been little studied. One environmental effect is trail bifurcation asymmetry. Ants forage on branching trail networks and must often decide which branch to take at a junction (bifurcation). This is an important decision, as finding food sources relies on making the correct choices at bifurcations. Bifurcation angle may provide important information when making this choice. We used a Y-maze with a pivoting 90° bifurcation to study trail choice of Lasius niger foragers at varying branch asymmetries (0°, [both branches 45° from straight ahead], 30° [branches at 30° and 60° from straight ahead], 45°, 60° and 90° [one branch straight ahead, the other at 90°]). The experiment was carried out either with equal amounts of trail pheromone on both branches of the bifurcation or with pheromone present on only one branch. Our results show that with equal pheromone, trail asymmetry has a significant effect on trail choice. Ants preferentially follow the branch deviating least from straight, and this effect increases as asymmetry increases (47% at 0°, 54% at 30°, 57% at 45°, 66% at 60° and 73% at 90°). However, when pheromone is only present on one branch, the graded effect of asymmetry disappears. Overall, however, there is an effect of asymmetry as the preference of ants for the pheromone-marked branch over the unmarked branch is reduced from 65%, when it is the less deviating branch, to 53%, when it is the more deviating branch. These results demonstrate that trail asymmetry influences ant decision-making at bifurcations and that this information interacts with trail pheromone presence in a non-hierarchical manner.
Acute enantioselective toxicity of fipronil and its desulfinyl photoproduct to Ceriodaphnia dubia

Fipronil is a phenylpyrazole insecticide increasingly used in applications such as rice culture, turf grass management, and residential pest control, with a high probability to contaminate aquatic environments. As a chiral pesticide, fipronil is released to the environment as a racemic mixture (equal amounts of optical isomers called enantiomers). Enantiomers can have different toxicological and biological activity; however, information on these differences, which is necessary for accurate risk assessment of chiral pesticides, is limited. Here we examine the acute toxicity of fipronil enantiomers, the racemate, and its photoproduct (desulfinyl fipronil) to Ceriodaphnia dubia. The 48‐h median lethal concentration (LC50) values based on measured concentrations of each compound indicate the (+) enantiomer (LC50 = 10.3 ± 1.1 μg/L, mean ± standard error [SE]) was significantly more toxic to C. dubia than either the (−) enantiomer (LC50 = 31.9 ± 2.2 μg/L) or racemate (LC50 = 17.7 ±1.3 μg/L). To account for any potential loss of fipronil through photolysis, tests were performed under light (fluorescent) and dark exposure conditions, and no significant differences in toxicity were observed. Desulfinyl fipronil, the major photodegradation product, which is not chiral, was detected at <1% of each parent compound in test solutions after 48 h. Separate toxicity tests with desulfinyl fipronil found a >20‐fold higher LC50 (355 ± 9.3 μg/L) compared to the fipronil racemate, suggesting lower adverse effects to C. dubia as a result of fipronil photolysis. The present results suggest selection of the (−) enantiomer in fipronil production for lower impacts to C. dubia; however, the consistency and relevancy of fipronil's enantiomer‐specific activity at both acute and chronic levels of concern to additional target and nontarget species needs further consideration.
Transfer of the Rf-1 region from FHH onto the ACI background increases susceptibility to renal impairment.

The genetically hypertensive fawn-hooded (FHH/Eur) rat is characterized by the early presence of systolic and glomerular hypertension, progressive proteinuria (UPV), and albuminuria (UAV), and focal glomerulosclerosis, resulting in premature death from renal failure. Previous studies showed that at least five genetic loci (Rf-1 to Rf-5) were linked to the development of renal impairment. Of these five, Rf-1 appears to play a major role. To study the impact of Rf-1 in the absence of the other loci, we transferred the Rf-1 region of chromosome 1, between the markers D1Mit34 and D1Rat156, Rf-1B for short, onto the genomic background of the normotensive August x Copenhagen Irish (ACI) rat. In this congenic strain, named ACI.FHH-D1Mit34/Rat156 or ACI.FHH-Rf1B, we challenged the renal hemodynamic function of these animals by studying the effects of unilateral nephrectomy (UNX) alone, or combined with N(G)-nitro-L-arginine methyl ester (L-NAME)-induced hypertension. Following UNX, the congenic strain developed significantly more UPV and UAV than the ACI progenitor. The differences were even more pronounced when UNX was combined with an L-NAME-induced rise in systolic blood pressure to about 150 mmHg, i.e., the level of hypertension present in the parental FHH strain. These findings indicate that the Rf-1B region of the FHH rat contains at least one gene affecting the susceptibility to progressive renal failure, especially in the presence of an increase in blood pressure.
The serializability problem for a temporal logic of transaction queries

We define the logic FOTLT(n), to be a monadic monodic fragment of first-order linear temporal logic, with 2n propositions representing the read and write steps of n two-step concurrent database transactions and a time-dependent predicate representing queries giving the sets of data items accessed by those read and write steps at given points in time. The models of FOTLT(n) contain interleaved sequences of the steps of infinitely many occurrences of the n transactions accessing unlimited data over time. A property of serializability is specified for FOTLT(n) formulae. We show that the serializability problem for FOTLT(n) formulae is decidable.
Intra-laboratory Comet Assay Sample Scoring Exercise for Determination of Formamidopyrimidine DNA Glycosylase Sites in Human Mononuclear Blood Cell DNA

Oxidative DNA damage detected by the comet assay as formamidopyrimidine DNA glycosylase (FPG) senstitive sites, almost as a rule is reported as comet assay score rather than numerical sites in the genome, probably because the latter requires X-ray calibration. We compared the ability of five experienced and five inexperienced comet assay investigators to detect a dose-response relationship in irradiated A549 lung epithelial cell culture samples (0, 10 Gy and three samples of 5 Gy), based on an arbitrary five class scoring system. The samples were scored on three different occasions, thus allowing determination of the variation in sample scoring. All investigators qualitatively distinguished between samples in a dose-dependent manner, albeit with large variation in the slope and intercept of dose-response curves. There was a tendency that investigators with experience in scoring A549 cells had more consistent results than experienced investigators who had only scored lymphocytes or inexperienced investigators. The inexperienced investigators improved their scoring ability during the three sessions. Subsequently we showed that the variation in baseline level of FPG modifications in mononuclear blood cells of five healthy humans was lower when investigators used their individual X-ray calibration curve as compared to a common calibration curve. In conclusion, this study showed that comet assay investigators score differently when using a five class scoring system, which indicates that more consistent estimations of FPG sites in the genome are obtained by use of investigators' individual X-ray calibrations.
SPOTT : A Mobile Robot Control Architecture forUnknown or Partially Known

A robot control architecture called SPOTT 1 is proposed and implemented as a real-time and parallel system of concurrently executing and cooperating modules. SPOTT provides a bridge for linking behavioral (i.e., reactive) and symbolic control. The control system is a real-time AI system which is responsible for dynamically adapting to changing environmental circumstances in order to successfully execute and complete a set of navigational tasks for an autonomous mobile robot. SPOTT consists of a be-havioral controller, a local dynamic path planner, and a global path planner, as well as a map and a graphical user interface. The behavioral control formalism is called TR+ and is based on an adaptation and extension of the Teleo-Reactive (TR) formalism introduced by Nils Nilsson. TR+ rules make decisions which aaect actuator control and map database maintenance. A dynamic local path planner continually polls the map database in order to navigate around newly encountered obstacles. The local dynamic path planner is based on a potential eld method using harmonic functions, which are guaranteed to have no spurious local minima. The global planning module advises the local planning module of the eeects of a global goal. We have developed a real-time parallel implementation of SPOTT using a message passing software package called PVM. Nav-igational experiments have consisted of moving the robot in an ooce and laboratory environment to known and unknown spatial locations with no or a partial a priori map.
BCE: Extracting Botnet Commands from Bot Executables

Botnets are a major threat to the security of computer systems and the Internet. An increasing number of individual Internet sites have been compromised by attacks from all across the world to become part of various kinds of malicious botnets. The Internet security research communi ty has made significant efforts to identify botnets, to collectdata on their activities, and to develop techniques for detectio n, mitigation, and disruption. One way of analyzing the behavi or of bots is to run the bot executables and observe their action s. For this to be possible, one needs proper input commands that trigger malicious behaviors. However, it is difficult and timeconsuming to manually infer botnet commands from binaries. In this paper, we present a tool calledBCE for automatically extracting botnet-command information from bot executables. Our experiments showed that the new search strategies developed forBCE yielded both substantially higher coverage of the parts of the program relevant to identifying bot commands, as well as lowered run-time. Keywords-botnet analysis; bot-command analysis; directed test generation; control dependence
Dynamic Spectrum Management for Multiple-Antenna Cognitive Radio Systems: Designs with Imperfect CSI

In this paper, we study the problem of resource allocation and optimization for multiple-input multiple-output (MIMO) cognitive radio (CR) systems under the assumption of imperfect channel state information (CSI) of the channels between the secondary users (SUs) and the primary users (PUs) at the SUs. We formulate robust design optimization problems for CR systems with one or more SUs communicating over a single or multiple frequency carriers in the presence of multiple PUs. We propose a linear matrix inequality (LMI) transformation that facilitates proper treatment of channel uncertainty at the SU transmitter and we provide solutions to the design problems based on convex optimization and Lagrange dual decomposition techniques. Finally, we demonstrate the importance of the proposed formulations and the implications of ignoring channel uncertainties when designing for CR systems.
In vivo cellular uptake of glutamate is impaired in the rat hippocampus during and after transient cerebral ischemia: A microdialysis extraction study

Using microdialysis in CA1 of the rat hippocampus, we studied the effect of transient cerebral ischemia on in vivo uptake and on extracellular levels of glutamate during, and at different time points after ischemia. 3H‐D‐aspartate (test substance), and 14C‐mannitol (reference substance), were added to the dialysis perfusate, and the cellular extraction of 3H‐D‐aspartate was calculated from scintillation analysis of fractionated dialysate samples. The extraction of 3H‐D‐aspartate was studied both in a tracer like condition with a perfusate concentration of 0.2 μM, and in a condition of high saturation level, with 1.0 mM D‐aspartate added to the perfusate. In between radioisotope perfusions, dialysate was sampled for analysis of amino acid content by HPLC. During ischemia, extraction of 3H‐D‐aspartate (0.2 μM) declined to a maximum reduction of 68%. In the hours after ischemia, extraction of 3H‐D‐aspartate (0.2 μM) was decreased by 32%. In the days after ischemia, there was a progressive decline in extraction of 3H‐D‐aspartate (1.0 mM), reaching a reduction of 89% on Day 4 after ischemia. Extracellular glutamate remained at control levels at all time points after ischemia. The present study is the first to investigate uptake of glutamate in the intact rat brain in relation to cerebral ischemia. Evidence is provided that uptake of Glu is restrained during ischemia, and that in the hours after ischemia, the extracellular turnover of glutamate is decreased. In the course of the days after ischemia, degeneration of CA1 pyramidal cells occurs concomitantly with a progressive decline in glutamate transport ability, possibly of pathogenetic importance to CA1 pyramidal cell loss. J Neurosci. Res. 66:1118–1126, 2001. © 2001 Wiley‐Liss, Inc.
Regulation of Ca2+ and Na+ in Normal and Failing Cardiac Myocytes

Abstract: Ca2+ in cardiac myocytes regulates contractility and relaxation, and Ca2+ and Na +regulation are linked via Na+/Ca2+ exchange (NCX). Heart failure (HF) is accompanied by contractile dysfunction and arrhythmias, both of which may be due to altered cellular Ca2+ handling. Smaller Ca2+ transient and sarcoplasmic reticulum (SR) Ca2+ content cause systolic dysfunction in HF. The reduced SR Ca2+ content is due to: (a) reduced SR Ca2+‐ATPase function (which also contributes to diastolic dysfunction), (b) increased expression and function of NCX (which competes with SR Ca2+‐ATPase during relaxation, but preserves diastolic function), and (c) enhanced diastolic SR Ca2+ leak. Relative contributions of these may vary with HF etiology and stage. Triggered arrhythmias (e.g., delayed afterdepolarizations [DADs]) are prominent in HF. DADs are due to spontaneous SR Ca2+ release and consequent activation of transient inward NCX current, which in HF allows DADs to more readily trigger arrhythmogenic action potentials. Thus NCX and Na+ are critical in systolic and diastolic function and arrhythmias. [Na+]i is elevated in HF, which may limit SR unloading and provide some Ca2+ influx during the HF action potential, thus limiting the depression of systolic function. High [Na+]i in HF is due to enhanced Na+ influx. Cellular Na+/K+‐ATPase (NKA) function appears unaltered, despite reduced NKA expression. This dichotomy led us to test NKA regulation by phospholemman (PLM). We find that PLM regulates NKA in a manner analogous to phospholamban regulation of SR Ca2+‐ATPase (i.e., inhibition that is relieved by PLM phosphorylation). We measured intermolecular FRET between PLM and NKA, which is reduced upon PLM phosphorylation. The lower expression level of more phosphorylated PLM in HF may explain the above dichotomy. Thus, altered Ca2+ and Na+ handling contributes to altered contractile function and arrhythmogenesis in HF.
Loop Closing in Topological Maps

In order to create consistent maps of unknown environments, a robot must be able to recognize when it has returned to a previously visited place. In this paper, we introduce an evidential approach to the loop-closing problem for topological maps, based on the Dempster-Shafer theory of evidence. In our approach, the robot makes a hypothesis whenever it may have revisited a place. It then attempts to verify hypotheses by continuing to traverse the environment, gathering evidence that supports (or refutes) the hypotheses. We describe methods for managing belief about multiple loop-closing hypotheses, and for determining a belief assignment given a piece of evidence. We also discuss methods for reducing the false alarm rate of our loop-closing algorithm, and provide simulated and real-world experimental results that verify the effectiveness of our approach.
Personalized Procedural Content Generation to Minimize Frustration and Boredom Based on Ranking Algorithm

A growing research community is working towards procedurally generating content for computer games and simulation applications with various player modeling techniques. In this paper, we present a two-step procedural content generation framework to minimize players' frustration and/or boredom according to player feedback and gameplay features. In the first step, we dynamically categorize the player styles based on a simple questionnaire beforehand and the gameplay features. In the second step, two player models (frustration and boredom) are built for each player style category. A ranking algorithm is utilized for player modeling to address two problems inherent in player feedback: inconsistency and inaccuracy. Experiment results on a testbed game show that our framework can generate less boring/frustrating levels with very high probabilities.
Principles and methods of testing finite state machines-a survey

With advanced computer technology, systems are getting larger to fulfill more complicated tasks: however, they are also becoming less reliable. Consequently, testing is an indispensable part of system design and implementation; yet it has proved to be a formidable task for complex systems. This motivates the study of testing finite stare machines to ensure the correct functioning of systems and to discover aspects of their behavior. A finite state machine contains a finite number of states and produces outputs on state transitions after receiving inputs. Finite state machines are widely used to model systems in diverse areas, including sequential circuits, certain types of programs, and, more recently, communication protocols. In a testing problem we have a machine about which we lack some information; we would like to deduce this information by providing a sequence of inputs to the machine and observing the outputs produced. Because of its practical importance and theoretical interest, the problem of testing finite state machines has been studied in different areas and at various times. The earliest published literature on this topic dates back to the 1950's. Activities in the 1960's mid early 1970's were motivated mainly by automata theory and sequential circuit testing. The area seemed to have mostly died down until a few years ago when the testing problem was resurrected and is now being studied anew due to its applications to conformance testing of communication protocols. While some old problems which had been open for decades were resolved recently, new concepts and more intriguing problems from new applications emerge. We review the fundamental problems in testing finite state machines and techniques for solving these problems, tracing progress in the area from its inception to the present and the stare of the art. In addition, we discuss extensions of finite state machines and some other topics related to testing.
Hotelling under Pressure

We show that oil production from existing wells in Texas does not respond to oil prices, while drilling activity and costs respond strongly. To explain these facts, we reformulate Hotelling’s classic model of exhaustible resource extraction as a drilling problem: firms choose when to drill, but production from existing wells is constrained by reservoir pressure, which decays as oil is extracted. The model implies a modified Hotelling rule for drilling revenues net of costs, explains why the production constraint typically binds, and rationalizes regional production peaks and observed patterns of prices, drilling, and production following demand and supply shocks.