Miracle-dz/UniFAR-FTUs huggingface dataset:
Extending graph homomorphism and simulation for real life graph matching

Among the vital problems in a variety of emerging applications is the graph matching problem, which is to determine whether two graphs are similar, and if so, find all the valid matches in one graph for the other, based on specified metrics. Traditional graph matching approaches are mostly based on graph homomorphism and isomorphism, falling short of capturing both structural and semantic similarity in real life applications. Moreover, it is preferable while difficult to find all matches with high accuracy over complex graphs. Worse still, the graph structures in real life applications constantly bear modifications. In response to these challenges, this thesis presents a series of approaches for efficiently solving graph matching problems, over both static and dynamic real life graphs. Firstly, the thesis extends graph homomorphism and subgraph isomorphism, respectively, by mapping edges from one graph to paths in another, and by measuring the semantic similarity of nodes. The graph similarity is then measured by the metrics based on these extensions. Several optimization problems for graph matching based on the new metrics are studied, with approximation algorithms having provable guarantees on match quality developed. Secondly, although being extended in the above work, graph matching is defined in terms of functions, which cannot capture more meaningful matches and is usually hard to compute. In response to this, the thesis proposes a class of graph patterns, in which an edge denotes the connectivity in a data graph within a predefined number of hops. In addition, the thesis defines graph pattern matching based on a notion of bounded simulation relation, an extension of graph simulation. With this revision, graph pattern matching is in cubic-time by providing such an algorithm, rather than intractable. Thirdly, real life graphs often bear multiple edge types. In response to this, the thesis further extends and generalizes the proposed revisions of graph simulation to a more powerful case: a novel set of reachability queries and graph pattern queries, constrained by a subclass of regular path expressions. Several fundamental problems of the queries are studied: containment, equivalence and minimization. The enriched reachability query does not increase the complexity of the above problems, shown by the corresponding algorithms. Moreover, graph pattern queries can be evaluated in cubic time, where two such algorithms are proposed. Finally, real life graphs are frequently updated with small changes. The thesis investigates incremental algorithms for graph pattern matching defined in terms of graph simulation, bounded simulation and subgraph isomorphism. Besides studying the results on the complexity bounds, the thesis provides the experimental study verifying that these incremental algorithms significantly outperform their batch counterparts in response to small changes, using real-life data and synthetic data.
Group foraging increases foraging efficiency in a piscivorous diver, the African penguin

Marine piscivores have evolved a variety of morphological and behavioural adaptations, including group foraging, to optimize foraging efficiency when targeting shoaling fish. For penguins that are known to associate at sea and feed on these prey resources, there is nonetheless a lack of empirical evidence to support improved foraging efficiency when foraging with conspecifics. We examined the hunting strategies and foraging performance of breeding African penguins equipped with animal-borne video recorders. Individuals pursued both solitary as well as schooling pelagic fish, and demonstrated independent as well as group foraging behaviour. The most profitable foraging involved herding of fish schools upwards during the ascent phase of a dive where most catches constituted depolarized fish. Catch-per-unit-effort was significantly improved when targeting fish schools as opposed to single fish, especially when foraging in groups. In contrast to more generalist penguin species, African penguins appear to have evolved specialist hunting strategies closely linked to their primary reliance on schooling pelagic fish. The specialist nature of the observed hunting strategies further limits the survival potential of this species if Allee effects reduce group size-related foraging efficiency. This is likely to be exacerbated by diminishing fish stocks due to resource competition and environmental change.
Expression of human cathepsin D in Xenopus oocytes: phosphorylation and intracellular targeting

We have obtained expression of a cDNA clone for human cathepsin D in Xenopus laevis oocytes. Biosynthetic studies with [35S]methionine labeling demonstrated that most of the cathepsin D remained intracellular and underwent proteolytic cleavage, converting a precursor of Mr 47,000 D to a mature form of Mr 39,000 D with processing intermediates of Mr 43,000-41,000 D. greater than 90% of the cathepsin D synthesized by oocytes bound to a mannose 6-phosphate (Man- 6-P) receptor affinity column, indicating the presence of phosphomannosyl residues. An analysis of [2-3H]mannose-labeled oligosaccharides directly demonstrated phosphomannosyl residues on cathepsin D. Sucrose-gradient fractionation, performed to define the membranous compartments that cathepsin D traversed during its biosynthesis, demonstrated that cathepsin D is targeted to a subpopulation of yolk platelets, the oocyte equivalent of a lysosome. Xenopus oocytes were able to endocytose lysosomal enzymes from the medium and this uptake was inhibited by Man-6-P, thus demonstrating the presence of Man-6-P receptors in these cells. Therefore, the entire Man- 6-P dependent pathway for targeting of lysosomal enzymes is present in the oocytes. Xenopus oocytes should be a useful system for examining signals responsible for the specific targeting of lysosomal enzymes to lysosomes.
Early referral recommendation for newly diagnosed rheumatoid arthritis: evidence based development of a clinical guide

Background: Effective treatment of active rheumatoid arthritis (RA) requires early diagnosis and early disease modifying antirheumatic drug (DMARD) treatment to have an impact on long term morbidity and mortality. Clinical criteria would facilitate early referral of the patient with suspected RA to a rheumatologist for definitive diagnosis and initiation of DMARD treatment at that point in the disease most likely to have an impact on the long term outcome. Objective: To develop a referral recommendation that may serve as a clinical guide for primary care doctors, enabling them to identify patients with suspected RA during the early inflammatory stages. Methods: Key points of the referral criteria were formed based on a thorough literature review targeting early RA, early arthritis clinics, DMARD treatment for early RA, prognostic factors of disease progression, early RA clinical trials, and quality of life. Evidence was graded using the methods defined by Shekelle et al. A draft version of the criterion was circulated among the authors for critical evaluation. A consensus integrated these comments. Results: Clinical evidence strongly supports the observations that structural damage occurs early in active RA and that early DMARD treatment improves the long term outcome of the disease. The observations indicate that rapid referral to a rheumatologist is advised when RA is suspected. This may be supported by the presence of any of the following: ≥3 swollen joints, metatarsophalangeal/metacarpophalangeal involvement, and morning stiffness of ≥30 minutes. Conclusion: The proposed early referral recommendation is a viable tool for primary care doctors to identify potential patients with active RA early in the disease. Early referral to a rheumatologist for definitive diagnosis and early DMARD treatment should improve the long term outcome of RA.
Der Umgang des Mittelstands mit neugestalteten und modernisierten Ausbildungsordnungen

Die Dynamik des wirtschaftlichen Strukturwandels in den neunziger Jahren loste auch im Berufsbildungssystem einen ordnungspolitischen Wandel aus. Geanderte Ausbildungsordnungen und Prufungskonzepte nehmen Einfluss auf die betriebliche Ausbildungspraxis. Die Studie untersucht daher, welche Auswirkungen die modernisierten Ausbildungs- und Prufungsordnungen auf den Mittelstand haben. Hierzu wird neben einer theoretischen auch eine empirische Auseinandersetzung mit dem Thema erfolgen. Die Auswertung einer eigenen Unternehmensbefragung aus dem Jahre 2002 wird um externe Studienergebnisse erweitert und durch gezielte Tiefeninterviews erganzt. Die Studie stellt im Ergebnis eine schwierige Handhabbarkeit der Ausbildungsordnungen in den Unternehmen fest, die sich aber nur zum Teil aus der Neugestaltung der Ausbildungsordnung ergibt. Schwerer wiegt die Diskrepanz zwischen der erwarteten und der tatsachlich vorhandenen Qualifikation der Jugendlichen, vor allem in kleinen Unternehmen. Die Diskrepanz wird insbesondere bei Handwerksbetrieben registriert, fuhrt jedoch nicht zu einer Einschrankung der Ausbildungsaktivitaten, sondern zu erhohtem Ausbildungsaufwand. Bereits vorhandene, branchen- und grosenspezifische Nachteile bei der Rekrutierung von Auszubildenden verscharften sich durch die Neuordnung weiter. Die Autoren stellen fest, dass ein Bedarf an Ausbildungsgangen fur mittelqualifizierte Tatigkeiten besteht. Deshalb wird die Einfuhrung von weniger anspruchsvollen Ausbildungsinhalten, um auch leistungsschwachere Jugendliche ausbilden zu konnen, befurwortet. Die Autoren bestatigen ebenfalls ein groses Straffungspotenzial im Neuordnungsverfahren von Ausbildungsordnungen, in das die Interessen mittelstandischer Betriebe besser integriert werden sollten. Des weiteren ist eine intensivere Verbindung zwischen Theorie und Praxis erforderlich.
Deep Reinforcement Learning with Regularized Convolutional Neural Fitted Q Iteration

We review the deep reinforcement learning setting, in which an agent receiving high-dimensional input from an environment learns a control policy without supervision using multilayer neural networks. We then extend the Neural Fitted Q Iteration value-based reinforcement learning algorithm (Riedmiller et al) by introducing a novel variation which we call Regularized Convolutional Neural Fitted Q Iteration (RCNFQ) that incorporates convolutional neural networks similarly to the Deep Q Network algorithm (Mnih et al) and dropout regularization to improve generalization performance. Finally, we present an implementation of the algorithm and discuss several extensions.
Characterization of Request Sequences for List Accessing Problem and New Theoretical Results for MTF Algorithm

List Accessing Problem is a well studied research problem in the context of linear search. Input to the list accessing problem is an unsorted linear list of distinct elements along with a sequence of requests, where each request is an access operation on an element of the list. A list accessing algorithm reorganizes the list while processing a request sequence on the list in order to minimize the access cost. Move-To-Front algorithm has been proved to be the best performing list accessing online algorithm till date in the literature. Characterization of the input request sequences corresponding to practical real life situations is a big challenge for the list accessing problem. As far as our knowledge is concerned, no characterization for the request sequences has been done in the literature till date for the list accessing problem. In this paper, we have characterized the request sequences for the list accessing problem based on several factors such as size of the list, size of the request sequence, ordering of elements and frequency of occurrence of elements in the request sequence. We have made a comprehensive study of MTF list accessing algorithm and obtained new theoretical results for our characterized special class of request sequences. Our characterization will open up a new direction of research for empirical analysis of list accessing algorithms for real life inputs.
Cardiovascular abnormalities with normal blood pressure in tissue kallikrein-deficient mice

Tissue kallikrein is a serine protease thought to be involved in the generation of bioactive peptide kinins in many organs like the kidneys, colon, salivary glands, pancreas, and blood vessels. Low renal synthesis and urinary excretion of tissue kallikrein have been repeatedly linked to hypertension in animals and humans, but the exact role of the protease in cardiovascular function has not been established largely because of the lack of specific inhibitors. This study demonstrates that mice lacking tissue kallikrein are unable to generate significant levels of kinins in most tissues and develop cardiovascular abnormalities early in adulthood despite normal blood pressure. The heart exhibits septum and posterior wall thinning and a tendency to dilatation resulting in reduced left ventricular mass. Cardiac function estimated in vivo and in vitro is decreased both under basal conditions and in response to βadrenergic stimulation. Furthermore, flow-induced vasodilatation is impaired in isolated perfused carotid arteries, which express, like the heart, low levels of the protease. These data show that tissue kallikrein is the main kinin-generating enzyme in vivo and that a functional kallikrein–kinin system is necessary for normal cardiac and arterial function in the mouse. They suggest that the kallikrein–kinin system could be involved in the development or progression of cardiovascular diseases.
Hemin, an iron‐binding porphyrin, inhibits HIF‐1α induction through its binding with heat shock protein 90

Hypoxia and growth factor stimulation induce hypoxia‐inducible factor‐1α (HIF‐1α), conferring upon cancer cells the ability to adapt to microenvironments and enhance proliferation, angiogenesis and metastasis. Hemin, an iron‐binding porphyrin, has been used to treat porphyria attacks, particularly in acute intermittent porphyria. Although the anti‐inflammatory and antitumor effects of hemin were reported, no information is available regarding its effect on HIF‐1α. Our study investigated whether hemin and other protoporphyrin compounds have the ability to inhibit HIF‐1α activity, and if so, what is the molecular basis of inhibition. Hemin treatment prevented CoCl2‐induced HIF‐1α expression. HIF‐1α inhibition by hemin resulted from an increase in its facilitated ubiquitination and degradation, as shown by the experimental results using cychloheximide treatment and ubiquitination assays. Consistently, hemin repressed HIF‐1α‐dependent gene transactivation. Intriguingly, hemin directly impeded the binding between heat shock protein 90 (HSP90) and HIF‐1α, which was reversed by the addition of an excess amount of ATP required for HSP90 activity. In addition, hemin decreased the expression of client proteins of HSP90. Thus, the inhibition of HIF‐1α activity by hemin might result from its interaction with HSP90. Moreover, treatment of protoporphyrin IX, ZnPP or Co(III)PP, but not Mn(III)PP, inhibited HIF‐1α induction, indicating that protoporphyrin ring in association with the nature of binding metal leads to HSP90 inhibition. In an in vivo model, hemin treatment inhibited not only the formation of new vessels but also cancer cell proliferation and migration/invasion, supporting the notion that hemin may be applied to the prevention and/or treatment of angiogenesis and/or cancer metastasis.
Evolutionary coupling in the KV1.2-β2 complex

KV1.2 is a potassium channel protein whose electrophysiological properties, including an oxygen sensing response, are modulated by auxiliary beta subunits. The beta subunits are homologous to oxidoreductases, supporting a hypothesis that the coupling of the two subunits helps connect the redox state of the cell to the electrical activity of the membrane. However the exact mechanism of the coupling has not been discovered to-date. We apply evolutionary correlation analysis to infer previously unknown components of the interaction network regulating the response to hypoxia of the KV1.2/β2 complex. Briefly, evolutionary correlation analysis involves finding correlated amino acid substitutions in functionally equivalent proteins (for both subunits) across a range of species. The method thus depends on a reliable method of inferring functionally equivalent (orthologous) proteins in different species, which method we describe in a paper recently published in PLoS ONE. One key finding is the characterization of a network of motif interactions between the α and the β subunits. By significance testing, we show that the likelihood of the correlations shown in the KV1.2-β2 two interaction motifs arising by chance is less than 0.0003, which shows that the correlations are statistically highly significant. We therefore believe that the correlations are likely to be biologically relevant. Other major findings are correlations between specific motifs in the KV1.2-β2 complex and motifs in other proteins such as RACK1 and Eif36sip, which in turn are connected to the hypoxia response. Our paper combines this correlation with the literature evidence on potassium channel inactivation and hypoxia response to identify specific motifs to serve as experimental targets for studies focused on this response. This work aims to add to our general understanding of two major issues in ion channel science: 1) how multi-protein complexes including ion channels function in coordinated fashion, and 2) how ion channels mediate the conversation between the intracellular and extracellular environments. We also aim to apply to ion channel science the principle that domain-domain interactions in proteins can be inferred from correlation of amino-acid substitutions in sets of functionally equivalent proteins.
Expression profile of the cadherin family in the developing Drosophila brain

The Drosophila genome encodes 17 members of the cadherin family of adhesion molecules, which in vertebrates has been implicated in patterning the nervous system through cell and axon sorting. With only a few exceptions all cadherins show widespread expression in the larval brain. What expression patterns have in common is that 1) they are global, in the sense that all lineages of the central brain or optic lobe, or both, show expression; and 2) expression is stage‐specific: some cadherins are expressed only in primary neurons (located closest to the neuropile), others in early secondary neurons (near the brain surface), or primaries plus late secondaries. The Fat‐like cadherins, Fat and Dachsous, as well as Cad96Ca and Cad74A, are expressed in the epithelial optic lobe anlagen, which matches the widespread epithelial expression of these molecules in the embryo. DE‐cadherin is restricted to immature secondary neurons and glia; by contrast, DN‐cadherin, Flamingo, Cad87A, Cad99C, and Calsyntenin‐1 appear in differentiating primary neurons and, at a later stage, some or all secondary neurons. Cad87A is strongly enriched apically in epithelia and in neuronal dendrites. Fat‐like, Cad86C, Cad88C, Cad89D, and Dret are expressed ubiquitously in embryonic and larval brains at low or moderate levels. We conclude from this analysis that cadherins are likely to play a role in ‘generic’ neural functions, such as neurite fasciculation, branching, and synapse formation. J. Comp. Neurol. 506:469–488, 2008. © 2007 Wiley‐Liss, Inc.
A Unified Coupling Model for Coupling Measurement in Object Oriented Software Systems

Coupling is the extent to which the functions performed by a subsystem are related. Low coupling is a characteristic of a well-designed subcomponent. The problem noted for research in this paper is lack of standardization of measures, ambiguity in definition of measures and poor conceptual links between coupling components. The key objective of this research paper is to propose a model for coupling measurement in object oriented software system. A review of related work is conducted on coupling frameworks. In this research data was collected from various software systems, analyzed using a Poisson distribution model and unified coupling model generated. From the model an algorithm was developed for assessing coupling in software systems. In conclusion coupling model of five components; object level coupling, static level coupling, dynamic and static level coupling is developed an algorithm proposed to support coupling measurement in object oriented software systems. In the unified model developed a coupling value of 0.049 and below indicates low coupling while a coupling value of 0.05 to 0.1 indicates high coupling in the software system.
Transient pass-transistor leakage current in SOI MOSFET's

This paper reports an accurate method of measuring the anomalous leakage current in pass-gate MOSFET's unique to SOI devices. A high-speed measurement setup is used to provide experimental results, and to quantify the magnitude of leakage. Particularly, great care is taken to measure only the device leakage current and not the currents due to parasitic capacitances. Systematic influences of different factors such as temperature, bias, device history, and device structure on this leakage current are experimentally established,.
Photoreaction of bacteriorhodopsin at high pH: origins of the slow decay component of M.

The absorption spectrum of light-adapted purple membrane in 3 M KCl is dependent on temperature even in the room temperature region. Temperature-induced difference spectra at various pH values suggested that the trans isomer of bacteriorhodopsin, bR570, is in thermal and/or photodynamic equilibrium with several different conformers. The major second conformer occurring at neutral pH had the same spectroscopic properties as the 13-cis isomer, and its content at 35 degrees C was estimated to be more than 20%. Heterogeneity in the protein conformation became more significant above pH8, where temperature-induced difference spectra exhibited a negative peak at 580 nm and a positive peak at 296 nm. This absorption change is very similar to that observed upon the formation of the N intermediate, suggesting that an N-like conformer occurs at high pH and temperature. A significant temperature dependence was also seen in the M decay kinetics at high pH, which were described by two decay components; i.e., the fast decaying M (Mf) was predominant at low temperature, but the amplitude of the slow component (M(s)) increased with increasing temperature. It is suggested that M(s) is generated upon excitation of the N-like conformer, in which the residue (Asp-96) usually acting as a proton donor to the Schiff base is deprotonated. The N-like conformer could be N itself, because M(s) was enhanced when N was accumulated by background light. A strong correlation between the amplitude of M(s) and the concentration of N was also revealed by the accumulation kinetics of Mf, M(s), and N after the onset of continuous actinic light. (ABSTRACT TRUNCATED AT 250 WORDS)
Characterizing and taming non-deterministic bugs in Javascript applications

JavaScript has become one of the most popular programming languages for both client-side and server-side applications. In JavaScript applications, events may be generated, triggered and consumed non-deterministically. Thus, JavaScript applications may suffer from non-deterministic bugs, when events are triggered and consumed in an unexpected order. In this proposal, we aim to characterize and combat non-deterministic bugs in JavaScript applications. Specifically, we first perform a comprehensive study about real-world non-deterministic bugs in server-side JavaScript applications. In order to facilitate bug diagnosis, we further propose approaches to isolate the necessary events that are responsible for the occurrence of a failure. We also plan to design new techniques in detecting non-deterministic bugs in JavaScript applications.