Miracle-dz/UniFAR-FTUs huggingface dataset:
Proteins involved in electron transfer to Fe(III) and Mn(IV) oxides by Geobacter sulfurreducens and Geobacter uraniireducens.

Whole-genome microarray analysis of Geobacter sulfurreducens grown on insoluble Fe(III) oxide or Mn(IV) oxide versus soluble Fe(III) citrate revealed significantly different expression patterns. The most upregulated genes, omcS and omcT, encode cell-surface c-type cytochromes, OmcS being required for Fe(III) and Mn(IV) oxide reduction. Other electron transport genes upregulated on both metal oxides included genes encoding putative menaquinol : ferricytochrome c oxidoreductase complexes Cbc4 and Cbc5, periplasmic c-type cytochromes Dhc2 and PccF, outer membrane c-type cytochromes OmcC, OmcG and OmcV, multicopper oxidase OmpB, the structural components of electrically conductive pili, PilA-N and PilA-C, and enzymes that detoxify reactive oxygen/nitrogen species. Genes upregulated on Fe(III) oxide encode putative menaquinol : ferricytochrome c oxidoreductase complexes Cbc3 and Cbc6, periplasmic c-type cytochromes, including PccG and PccJ, and outer membrane c-type cytochromes, including OmcA, OmcE, OmcH, OmcL, OmcN, OmcO and OmcP. Electron transport genes upregulated on Mn(IV) oxide encode periplasmic c-type cytochromes PccR, PgcA, PpcA and PpcD, outer membrane c-type cytochromes OmaB/OmaC, OmcB and OmcZ, multicopper oxidase OmpC and menaquinone-reducing enzymes. Genetic studies indicated that MacA, OmcB, OmcF, OmcG, OmcH, OmcI, OmcJ, OmcM, OmcV and PccH, the putative Cbc5 complex subunit CbcC and the putative Cbc3 complex subunit CbcV are important for reduction of Fe(III) oxide but not essential for Mn(IV) oxide reduction. Gene expression patterns for Geobacter uraniireducens were similar. These results demonstrate that the physiology of Fe(III)-reducing bacteria differs significantly during growth on different insoluble and soluble electron acceptors and emphasize the importance of c-type cytochromes for extracellular electron transfer in G. sulfurreducens.
Applications and Implications of Neutral versus Non-neutral Markers in Molecular Ecology

The field of molecular ecology has expanded enormously in the past two decades, largely because of the growing ease with which neutral molecular genetic data can be obtained from virtually any taxonomic group. However, there is also a growing awareness that neutral molecular data can provide only partial insight into parameters such as genetic diversity, local adaptation, evolutionary potential, effective population size, and taxonomic designations. Here we review some of the applications of neutral versus adaptive markers in molecular ecology, discuss some of the advantages that can be obtained by supplementing studies of molecular ecology with data from non-neutral molecular markers, and summarize new methods that are enabling researchers to generate data from genes that are under selection.
Workflow Execution in Disconnected Environments

Workflow management systems are frequently used for modeling, monitoring and controlling the coordinated execution of activities performed by workgroups in a variety of contexts. With the widespread use of portable computers and their growing computational power, conventional systems have often proved to be overly restrictive, effectively limiting the level of autonomy of the users involved. This paper identifies and analyzes different flexibilization techniques and mechanisms that can be employed in a workflow management system to better support disconnected operation. In order to test the viability of the ideas discussed, a system was built whose design met the requirements presented in the text and which allows the exploration of specific features of different kinds of workflow so as to enhance execution flexibility, without compromising the predefined structure. The system was developed in Java, which allows for portable execution and, with recent advances in compact virtual machines, enables it to run in an increasing number of devices.
Optimal Power Flow with steady-state voltage stability consideration using Improved Evolutionary Programming

This paper presents an Improved Evolutionary Programming (IEP) algorithm for the Optimal Power Flow (OPF) with steady-state voltage stability consideration. The objective function is formulated as a trade-off between an economic concern, i.e. fuel cost and a system security issue, i.e. voltage stability margin. The indicator L is adopted to estimate the steady-state voltage stability margin in this paper. The proposed IEP algorithm borrows an idea of crossover techniques from Real-Coded Genetic Algorithm (RCGA) to enhance the offspring generation process. The IEEE 30-bus system is used as the test system. Three types of cost curves are considered to verify that the proposed algorithm works well with both convex and non-convex objective functions. The results of the proposed method are compared with those of the EP algorithm, which solely relies on the mutation process for offspring generation. Moreover, a series of experiments are conducted to properly tune the main IEP parameters.
Changes in regional brain glucose metabolism measured with positron emission tomography after paroxetine treatment of major depression.

OBJECTIVE Depression is commonly associated with frontal hypometabolic activity accompanied by hypermetabolism in certain limbic regions. It is unclear whether successful antidepressant treatments reverse these abnormalities or create new resting levels of metabolism. The aim of the present study was to assess the effects of successful paroxetine treatment on regional glucose metabolism in patients with major depression. METHOD Positron emission tomography with [(18)F]fluorodeoxyglucose was performed on 13 male patients before and after 6 weeks of paroxetine therapy. Resting state scans were also acquired under similar conditions in 24 healthy male subjects for comparison. RESULTS After successful paroxetine therapy, increased glucose metabolism occurred in dorsolateral, ventrolateral, and medial aspects of the prefrontal cortex (left greater than right), parietal cortex, and dorsal anterior cingulate. Areas of decreased metabolism were noted in both anterior and posterior insular regions (left) as well as right hippocampal and parahippocampal regions. In comparison to metabolism levels in a group of healthy volunteers, the increase in prefrontal metabolic activity represented a normalization of previously reduced metabolic activity, whereas the reduction in pregenual anterior cingulate activity represented a decrease from previously elevated metabolic levels. CONCLUSIONS These results provide further support for a dysfunction in cortical-limbic circuitry in depression, which is at least partly reversed after successful paroxetine treatment.
Adaptive Monitoring to Detect Intrusions in Critical Servers

An intrusion in a critical server can affect the security of an entire infrastructure that relies on it, including clients and other services. Hence, there is a constant concern in deploying and maintaining the correct execution of these servers. This paper presents an approach for continuous monitoring of a server execution in an adaptive way, where fundamental tasks are thoroughly monitored, and compared against a previously inferred behavioral profile.
Fast Evaluation of Radial Basis Functions: Moment-Based Methods

This paper presents a new method for the fast evaluation of univariate radial basis functions of the form $s(x) = \sum_{n=1}^N d_n \phi ( | x -x_n | ) $ to within accuracy $\epsilon$. The method can be viewed as a generalization of the fast multipole method in which calculations with far field expansions are replaced by calculations involving moments of the data. The method has the advantage of being adaptive to changes in $\phi$. That is, with this method changing to a new $\phi$ requires only coding a one- or two-line function for the (slow) evaluation of $\phi$. In contrast, adapting the usual fast multipole method to a new $\phi$ involves much mathematical analysis of appropriate series expansions and corresponding translation operators, followed by a substantial amount of work expressing this mathematics in code.
On the Generalization Properties of Differential Privacy

A new line of work, started with Dwork et al., studies the task of answering statistical queries using a sample and relates the problem to the concept of differential privacy. By the Hoeffding bound, a sample of size $O(\log k/\alpha^2)$ suffices to answer $k$ non-adaptive queries within error $\alpha$, where the answers are computed by evaluating the statistical queries on the sample. This argument fails when the queries are chosen adaptively (and can hence depend on the sample). Dwork et al. showed that if the answers are computed with $(\epsilon,\delta)$-differential privacy then $O(\epsilon)$ accuracy is guaranteed with probability $1-O(\delta^\epsilon)$. Using the Private Multiplicative Weights mechanism, they concluded that the sample size can still grow polylogarithmically with the $k$. Very recently, Bassily et al. presented an improved bound and showed that (a variant of) the private multiplicative weights algorithm can answer $k$ adaptively chosen statistical queries using sample complexity that grows logarithmically in $k$. However, their results no longer hold for every differentially private algorithm, and require modifying the private multiplicative weights algorithm in order to obtain their high probability bounds. We greatly simplify the results of Dwork et al. and improve on the bound by showing that differential privacy guarantees $O(\epsilon)$ accuracy with probability $1-O(\delta\log(1/\epsilon)/\epsilon)$. It would be tempting to guess that an $(\epsilon,\delta)$-differentially private computation should guarantee $O(\epsilon)$ accuracy with probability $1-O(\delta)$. However, we show that this is not the case, and that our bound is tight (up to logarithmic factors).
Perceptions of college students of color about community service learning through tutoring

PERCEPTIONS OF COLLEGE STUDENTS OF COLOR ABOUT COMMUNITY SERVICE LEARNING THROUGH TUTORING SEPTEMBER 2003 KACIE CHARMION MCCOLLUM, B.A., BENEDICT COLLEGE M.Ed., UNIVERSITY OF MASSACHUSETTS AMHERST Ed.D. , UNIVERSITY OF MASSACHUSETTS AMHERST Directed by: Professor John C. Carey This study examines perceptions of college students of color about their community service (CS) experiences as tutors in public schools. It explores how Black and Latino students at one large public university and three small private colleges in the Northeast conceptualized their experiences as tutors, the impact of tutoring on their college education, and the affects of tutoring on their career choices. This study is significant because it enhances our knowledge of the experiences of students of color in CS activities. This study may generate information that is valid for the recruitment and retention of teachers of color and possibly open new avenues about the recipients of service. From a policy perspective, the information is potentially useful to CS organizations, colleges and universities, public and private schools, local, state, and federal policymakers. Three methods of inquiry are used: (1) Pre-questionnaires were used to ascertain * % a biographical background of each participant; (2) modified in-depth interviews were conducted with each participant; and (3) post-questionnaires provided opportunity for students to reflect on the pre-questionnaire and oral interview questions and draw further conclusions about their CS tutoring efforts. The research population included 14
Wave dispersion relations in Yukawa fluids.

The wave dispersion relations in the fluid phase of Yukawa systems are obtained from molecular dynamics (MD) simulations for a wide range of the parameters. The Yukawa system is a collection of particles interacting through Yukawa (i.e., screened Coulomb) potentials, which can serve as a simple model for dusty plasmas. Our simulations have clearly shown that the transverse wave dispersion has a cutoff at a long wavelength even in the case of weak screening. The MD simulation data are compared with earlier theoretical predictions of the Yukawa dispersion relations and the validity of these theories is clarified.
MAC for ad-hoc inter-vehicle network: services and performance

In this paper we analyze the performance of ADHOC MAC, a new MAC protocol proposed within CarTALK200, a European research project with the purpose to design novel solutions for inter-vehicle communications. ADHOC MAC has been devised to provide a reliable single hop broadcast channel overcoming the hidden terminal problem, and an effective multi hop broadcast service by exploiting the connectivity information provided by the protocol. The simulation results presented in the paper prove the effectiveness of ADHOC MAC in terms of access delay to the shared resource and resource reuse when considering a single hop broadcast service. The efficiency of the multi-hop broadcast service is compared through simulation with flooding and with a centralized greedy heuristics that gives an upper bound to the performance. Results show that the distributed ADHOC-MAC multi-hop broadcast mechanism performs closely to the centralized greedy heuristics.
Attentional Regulation in Young Twins with Probable Stuttering, High Nonfluency, and Typical Fluency

Purpose: Using a sample of 20,445 Dutch twins, this study examined the relationship between speech fluency and attentional regulation in children. A secondary objective was to identify etiological overlap between nonfluency and poor attention using fluency-discordant twin pairs. Method: Three fluency groups were created at age 5 using a parent questionnaire: Multiple scales assessing attention, primarily self-regulation/inhibition, were obtained from both parents when children were ages 5 and 7 and from teachers when children were age 7. Results: When compared with the TF controls, both the PS and HNF children received higher (i.e., more problematic) scores on parental attention ratings at both ages (p < .002). Effect sizes were moderate for both groups. Teacher and parent ratings were generally comparable. The discordant co-twin analyses suggested that nonfluency and attention were influenced by potentially overlapping genetic and shared environmental factors. Conclusions: The liability to express both high nonfluency and problems with self-regulation/inhibition may arise from a common set of pathogenic mechanisms. This supports emerging models of stuttering, which propose that poor fluency may be part of a broader network of impaired self-regulatory processes. R ecently, there has been increased interest in topics addressing the intersection between unstable fluency and attentional self-regulation in young children diagnosed with stuttering. Although most children who stutter (CWS) do not have frank attentional disorders, there is growing evidence that, relative to their fluency-normal peers, young CWS are more likely to be perceived by parents as having some attentional diffi-Among the attention-related problem behaviors that have been reported for CWS are high distractibility and difficulties with or slow a positive association between having ever stuttered and having an attention-deficit disorder has been reported in two retrospective studies of adults (Alm & Risberg, 2007; Biederman et al., 1993). Although these studies have provided suggestive evidence for a relationship between speech fluency and attentional regulation , no studies have provided a complete explanation for how these processes may intersect and whether they may be causally related.
Has our brain grown too big to think effectively

A variant of microcephalin, MCPH1 gene, was introgressed about 37,000 years ago into Homo sapiens genetic pool from an archaic (Homo erectus) lineage and rose to exceptionally high frequency of around 70 percent worldwide today. It is involved in regulating neuroblast proliferation and its changes alter the rate of division and/or differentiation of neuroblasts during the neurogenic phase of embriogenesis, which could alter the size and structure of the resulting brain. At the time of introgression, images had already been painted on the walls of caves and speech has been in use for over 100,000 years, as had been abstract thinking. Like today, reasoning and thinking were the primary faculties of individuals. Homo erectus either did not possess those faculties or was markedly inferior to Homo sapiens in them. Its brain was smaller and the cortex was apparently less convoluted. Thus, introgressed microcephalin allele directed neurogenesis evolutionary back to less complicated brain structure typical for our evolutionary forefathers, slightly decreasing the level of complexity already achieved by Homo sapiens 37,000 years ago. Despite that, it proliferated at a rapid pace. It yields a supposition: 37,000 years ago the brains of Homo sapiens were too big and too complicated for the kind of thinking needed for the highest fitness of individuals. Since adaptation cannot by definition surpass selection requirements, the volume and complication of the human brain did not originate under selective pressure to improve effective thinking and they cannot be explained in terms of such selection. A proposal to solve this quandary is presented, claiming that Homo sapiens originated just by chance. Endurance running led to the emergence of Homo sapiens. The human mind and larynx used for speech are side-effects of more than a million years of endurance running by pre-human hunters.
Chart Parsing and Constraint Programming

In this paper, parsing-as-deduction and constraint programming are brought together to outline a procedure for the specification of constraint-based chart parsers. Following the proposal in Shieber et al. (1995), we show how to directly realize the inference rules for deductive parsers as Constraint Handling Rules (Fruhwirth, 1998) by viewing the items of a chart parser as constraints and the constraint base as a chart. This allows the direct use of constraint resolution to parse sentences.
Structural characterisation of underivatised olive pulp xylo-oligosaccharides by mass spectrometry using matrix-assisted laser desorption/ionisation and electrospray ionisation.

Purified olive pulp glucuronoxylans, with a Xyl/GlcA ratio of 7:1, were subjected to mild acid hydrolysis and the mixture of oligosaccharides obtained was fractionated by size exclusion chromatography. One elution fraction representative of low molecular weight oligosaccharides was analysed by mass spectrometry using matrix-assisted laser desorption/ionisation (MALDI) and electrospray ionisation (ESI) as ionisation methods, in the positive mode. Both types of spectra showed cationised molecules [M + Na](+) of xylo-oligosaccharides in a range below m/z 1,000. The xylo-oligosaccharide structures identified were series of neutral oligosaccharides of xylose (Xyl(n), n = 3-7), of acidic oligosaccharides substituted by one glucuronic acid (Xyl(n)GlcA, n = 3-5) and by two glucuronic acid residues (Xyl(n)GlcA(2), n = 2 and 3), and also of acidic oligosaccharides substituted with one 4-O-methylglucuronic acid residue (Xyl(n)meGlcA, n = 2-4). The proposed structures were confirmed by tandem mass (MS/MS) spectra obtained using collision induced dissociation of the molecular ions. Fragmentation of cationised adducts of neutral Xyl(n) yielded C- and A-type fragments, while ammonium adducts mainly yielded B-type fragments. The fragmentation of the sodium adducts of acidic oligosaccharides (Xyl(n)meGlcA, Xyl(n)GlcA) resulted in the loss of the substituting residue (GlcA or meGlcA) as the predominant fragment, while the corresponding ammonium adducts yielded B-type fragments.
Sequence of Pathogenic Events in Cynomolgus Macaques Infected with Aerosolized Monkeypox Virus

ABSTRACT To evaluate new vaccines when human efficacy studies are not possible, the FDA's “Animal Rule” requires well-characterized models of infection. Thus, in the present study, the early pathogenic events of monkeypox infection in nonhuman primates, a surrogate for variola virus infection, were characterized. Cynomolgus macaques were exposed to aerosolized monkeypox virus (105 PFU). Clinical observations, viral loads, immune responses, and pathological changes were examined on days 2, 4, 6, 8, 10, and 12 postchallenge. Viral DNA (vDNA) was detected in the lungs on day 2 postchallenge, and viral antigen was detected, by immunostaining, in the epithelium of bronchi, bronchioles, and alveolar walls. Lesions comprised rare foci of dysplastic and sloughed cells in respiratory bronchioles. By day 4, vDNA was detected in the throat, tonsil, and spleen, and monkeypox antigen was detected in the lung, hilar and submandibular lymph nodes, spleen, and colon. Lung lesions comprised focal epithelial necrosis and inflammation. Body temperature peaked on day 6, pox lesions appeared on the skin, and lesions, with positive immunostaining, were present in the lung, tonsil, spleen, lymph nodes, and colon. By day 8, vDNA was present in 9/13 tissues. Blood concentrations of interleukin 1ra (IL-1ra), IL-6, and gamma interferon (IFN-γ) increased markedly. By day 10, circulating IgG antibody concentrations increased, and on day 12, animals showed early signs of recovery. These results define early events occurring in an inhalational macaque monkeypox infection model, supporting its use as a surrogate model for human smallpox. IMPORTANCE Bioterrorism poses a major threat to public health, as the deliberate release of infectious agents, such smallpox or a related virus, monkeypox, would have catastrophic consequences. The development and testing of new medical countermeasures, e.g., vaccines, are thus priorities; however, tests for efficacy in humans cannot be performed because it would be unethical and field trials are not feasible. To overcome this, the FDA may grant marketing approval of a new product based upon the “Animal Rule,” in which interventions are tested for efficacy in well-characterized animal models. Monkeypox virus infection of nonhuman primates (NHPs) presents a potential surrogate disease model for smallpox. Previously, the later stages of monkeypox infection were defined, but the early course of infection remains unstudied. Here, the early pathogenic events of inhalational monkeypox infection in NHPs were characterized, and the results support the use of this surrogate model for testing human smallpox interventions.
The combination of positive and negative feedback loops confers exquisite flexibility to biochemical switches

A wide range of cellular processes require molecular regulatory pathways to convert a graded signal into a discrete response. One prevalent switching mechanism relies on the coexistence of two stable states (bistability) caused by positive feedback regulations. Intriguingly, positive feedback is often supplemented with negative feedback, raising the question of whether and how these two types of feedback can cooperate to control discrete cellular responses. To address this issue, we formulate a canonical model of a protein–protein interaction network and analyze the dynamics of a prototypical two-component circuit. The appropriate combination of negative and positive feedback loops can bring a bistable circuit close to the oscillatory regime. Notably, sharply activated negative feedback can give rise to a bistable regime wherein two stable fixed points coexist and may collide pairwise with two saddle points. This specific type of bistability is found to allow for separate and flexible control of switch-on and switch-off events, for example (i) to combine fast and reversible transitions, (ii) to enable transient switching responses and (iii) to display tunable noise-induced transition rates. Finally, we discuss the relevance of such bistable switching behavior, and the circuit topologies considered, to specific biological processes such as adaptive metabolic responses, stochastic fate decisions and cell-cycle transitions. Taken together, our results suggest an efficient mechanism by which positive and negative feedback loops cooperate to drive the flexible and multifaceted switching behaviors arising in biological systems.