Miracle-dz/UniFAR-FTUs huggingface dataset:
Direct Actions of Urotensin II on the Heart: Implications for Cardiac Fibrosis and Hypertrophy

Abstract— Urotensin II (UII) is a somatostatin-like peptide recently identified as a potent vasoconstrictor. In this study, we examined whether UII promotes cardiac remodeling through nonhemodynamic effects on the myocardium. In a rat model of heart failure after myocardial infarction (MI), increased UII peptide and UII receptor protein expression was observed in both infarct and noninfarct regions of the left ventricle compared with sham. Moreover, post-MI remodeling was associated with a significant 75% increase in UII receptor gene expression in the heart (P <0.05 versus sham controls), with this increase noted in both regions of the left ventricle. In vitro, UII (10−7 mol/L) stimulation of neonatal cardiac fibroblasts increased the level of mRNA transcripts for procollagens &agr;1(I), &agr;1(III), and fibronectin by 139±15% (P <0.01), 59±5% (P <0.05), and 141±14% (P <0.01), respectively, with a concomitant 23±2% increase in collagen peptide synthesis as determined by 3H-proline incorporation (P <0.01). UII had no effect on cellular hypertrophy, as determined by changes in total protein content in isolated neonatal cardiomyocytes. However, expression of recombinant rat UII receptor in neonatal cardiomyocytes resulted in significant UII-dependent activation of hypertrophic signaling as demonstrated by increased total protein content (unstimulated, 122.4±4.0 &mgr;g/well; rat UII, 147.6±7.0 &mgr;g/well; P <0.01) and activation of the hypertrophic phenotype through G&agr;q- and Ras-dependent pathways. These results indicate that, in addition to potent hemodynamic effects, UII may be implicated in myocardial fibrogenesis through increased collagen synthesis by cardiac fibroblasts and may also be an important determinant of pathological cardiac hypertrophy in conditions characterized by UII receptor upregulation.
Analogies: Integrating Multiple Cognitive Abilities

Analogical reasoning has long been seen as a powerful way of extending the reach of ones knowledge. One product of analogical reasoning is analogical learning in which the result of the comparison increases our understanding of some domain. This work describes a method for learning new domain theories by analogy. We use analogies between pairs of problems and worked solutions to create a domain mapping between a familiar and a new domain. This mapping allows us to initialize the new domain. After this initialization, another analogy is made between the domain theories themselves providing additional conjectures about the new domain. An experiment is described where the system learns to solve rotational kinematics problems by analogy with translational kinematics problems, outperforming a version of the system that is incrementally given the correct domain theory.
Structure-Based Predictive Models for Allosteric Hot Spots

In allostery, a binding event at one site in a protein modulates the behavior of a distant site. Identifying residues that relay the signal between sites remains a challenge. We have developed predictive models using support-vector machines, a widely used machine-learning method. The training data set consisted of residues classified as either hotspots or non-hotspots based on experimental characterization of point mutations from a diverse set of allosteric proteins. Each residue had an associated set of calculated features. Two sets of features were used, one consisting of dynamical, structural, network, and informatic measures, and another of structural measures defined by Daily and Gray [1]. The resulting models performed well on an independent data set consisting of hotspots and non-hotspots from five allosteric proteins. For the independent data set, our top 10 models using Feature Set 1 recalled 68–81% of known hotspots, and among total hotspot predictions, 58–67% were actual hotspots. Hence, these models have precision P = 58–67% and recall R = 68–81%. The corresponding models for Feature Set 2 had P = 55–59% and R = 81–92%. We combined the features from each set that produced models with optimal predictive performance. The top 10 models using this hybrid feature set had R = 73–81% and P = 64–71%, the best overall performance of any of the sets of models. Our methods identified hotspots in structural regions of known allosteric significance. Moreover, our predicted hotspots form a network of contiguous residues in the interior of the structures, in agreement with previous work. In conclusion, we have developed models that discriminate between known allosteric hotspots and non-hotspots with high accuracy and sensitivity. Moreover, the pattern of predicted hotspots corresponds to known functional motifs implicated in allostery, and is consistent with previous work describing sparse networks of allosterically important residues.
Disposition of perfluorinated acid isomers in sprague‐dawley rats; Part 2: Subchronic dose

Two major industrial synthetic pathways have been used to produce perfluorinated acids (PFAs) or their precursors: Telomerization and electrochemical fluorination (ECF). Products of telomer and ECF origin can be distinguished by structural isomer profiles. A mixture of linear and branched perfluoroalkyl isomers is associated with ECF. Telomer products characteristically consist of a single perfluoroalkyl geometry, typically linear. In biota, it is unclear if the isomer profile is conserved relative to the exposure medium and hence whether PFA isomer profiles in organisms are useful for distinguishing environmental PFA sources. A companion study suggested isomer‐specific disposition following a single oral gavage exposure to rats. To confirm these findings under a more realistic subchronic feeding scenario, male and female rats were administered PFA isomers by diet for 12 weeks, followed by a 12‐week depuration period. The diet contained 500 ng/g each of ECF perfluorooctanoate (PFOA, ∼80% n‐PFOA), ECF perfluorooctane sulfonate (PFOS, ∼70% n‐PFOS), and linear and isopropyl perfluorononanoate (n‐ and iso‐PFNA). Blood sampling during the exposure phase revealed preferential accumulation of n‐PFOA and n‐PFNA compared to most branched isomers. Female rats depurated all isomers faster than males. Both sexes eliminated most branched perfluorocarboxylate isomers more rapidly than the n‐isomer. Elimination rates of the major branched PFOS isomers were not statistically different from n‐PFOS. Two minor isomers of ECF PFOA and one branched PFOS isomer had longer elimination half‐lives than the n‐isomers. Although extrapolation of these pharmacokinetics trends in rats to humans and wildlife requires careful consideration of dosage level and species‐specific physiology, cumulative evidence suggests that perfluorocarboxylate isomer profiles in biota may not be suitable for quantifying the relative contributions of telomer and ECF sources.
Hidden Markov Models in Bioinformatics with Application to Gene Finding in Human DNA 308-761 Machine Learning Project

A Hidden Markov Model (HMM) is a stochastic model that captures the statistical properties of observed real world data. A good HMM accurately models the real world source of the observed data and has the ability to simulate the source. Machine Learning techniques based on HMMs have been successfully applied to problems including speech recognition, optical character recognition, and as we will examine, problems in computational biology. The main computational biology problems with HMM-based solutions are protein family profiling, protein binding site recognition and the problem that is the topic of this paper, gene finding in DNA.
Cholecystokinin-A receptors modulate gastric sensory and motor responses to gastric distension and duodenal lipid.

BACKGROUND & AIMS The combination of duodenal lipid and gastric distention induces meal-like fullness followed by nausea in healthy subjects. The aim of this study was to assess the role of cholecystokinin (CCK) A receptors in these changes using a CCK-A antagonist loxiglumide. METHODS Twelve healthy subjects were studied on four occasions, during which either 0.9% saline or 20% Intralipid was infused intraduodenally on two occasions each (1 mL/min) while the proximal stomach was distended with air (100 mL/min). During each duodenal infusion, subjects received intravenous loxiglumide (10 mg.kg-1.h-1) on 1 day and placebo on the other. Intragastric pressure changes were recorded, and the subjects reported gastric sensations (fullness, nausea). RESULTS Loxiglumide did not influence gastric motility or sensitivity during duodenal saline infusion. Duodenal lipid reduced gastric tonic and phasic pressure activity during distensions and induced meal-like fullness and nausea; sensations were reported at similar volumes but lower intragastric pressures (P < 0.001 vs. saline). Loxiglumide partially restored gastric tonic and phasic activity during lipid infusion, reduced the occurrence of meal-like fullness and nausea, and increased the pressures at which sensations were reported (P < 0.001 vs. placebo). CONCLUSIONS CCK-A receptors are involved in the induction of meal-like fullness and nausea associated with intraduodenal lipid and gastric distention.
Hung Liang-Chi: A Chinese Malthus

Hung Liang-chi is well-known to Chinese scholars as a poet philosopher calligrapher historian and patriot. He has also been considered under the more generally arresting title of "Chinese Malthus". As such the wider demographic public only knows of him as a name and textbooks on population questions ignore him completely. A translation of his demographic essay is thus overdue; to-day they have a special fairly obvious interest. The growth of Chinas economy; the size of her population revealed in the recent census; and the frequent discussions of population birth control Malthusianism and their relevance to socialist China add point to what recent and past literature in China has had to say on the interrelation of population size and national welfare. The main body of traditional opinion in China viewing the vast under-developed parts of the economy has dwelt of course on the deficiency of population rather than on overpopulation. More people meant more taxpayers and more soldiers; more land could be put under cultivation; and the growth of the population was interpreted as a good index of increasing wealth. They represented increments in the social capital of the nation. But every now and then there was an unorthodox voice uneasy about the local rapid increase of population. Hung Liang-chi was such a writer. Moreover below the level of the literati the people themselves knew discussed and practiced a variety of measures which had the effect of slowing down the growth of population. Abstinence was sometimes practiced during marriage for the additional reason that it was said by the Buddhists and Taoists to prolong the length of life; and many other popular devices included to an extraordinary extent infanticide. Both Adam Smith and Malthus reported these practices. (excerpt)
Gamification of Software Testing

Writing good software tests is difficult, not everysoftware developer’s favorite occupation, and not a prominentaspect in programming education. However, human involvementin testing is unavoidable: What makes a test good is oftendown to intuition; what makes a test useful depends on anunderstanding of the program context; what makes a test findbugs depends on understanding the intended program behaviour.Because the consequences of insufficient testing can be dire, thispaper explores a new angle to address the testing problem:Gamification is the approach of converting potentially tediousor boring tasks to components of entertaining gameplay, wherethe competitive nature of humans motivates them to competeand excel. By applying gamification concepts to software testing,there is potential to fundamentally change software testing inseveral ways: First, gamification can help to overcome deficienciesin education, where testing is a highly neglected topic. Second,gamification engages practitioners in testing tasks they wouldotherwise neglect, and gets them to use advanced testing toolsand techniques they would otherwise not consider. Finally, gamificationmakes it possible to crowdsource complex testing tasksthrough games with a purpose. Collectively, these applications ofgamification have the potential to substantially improve softwaretesting practice, and thus software quality.
Salmonella enterica Serotype Choleraesuis: Epidemiology, Pathogenesis, Clinical Disease, and Treatment

SUMMARY Nontyphoid Salmonella strains are important causes of reportable food-borne infection. Among more than 2,000 serotypes, Salmonella enterica serotype Choleraesuis shows the highest predilection to cause systemic infections in humans. The most feared complication of serotype Cholearesuis bacteremia in adults is the development of mycotic aneurysm, which previously was almost uniformally fatal. The advances in diagnostic techniques, surgical care, and antimicrobial therapy have greatly improved the survival of these patients. However, the recent emergence of serotype Choleraesuis that is resistant to ampicillin, chloramphenicol, trimethoprim-sulfamethoxazole, and, notably, fluoroquinolone antibiotics has aroused concern about the use of these agents for the empirical treatment of systemic infection caused by this organism. In view of the serious implications of the situation, the chain of transmission and mechanism of resistance should be carefully studied to reduce the spread of infection and threat to human health. To date, there are no vaccines available to prevent serotype Choleraesuis infections in humans. The availability, in the near future, of the genome sequence of serotype Cholearesuis will facilitate the development of effective vaccines as well as the discovery of new targets for novel antimicrobial agents.
Novičarski Dejavniki in Internetna Družbena Omrežja

Povzetek V procesih stalnih preobrazb in nadgradenj novih tehnoloških/komunikacijskih platform in formatov tudi novinarstvo rekonfigurira svoj položaj v družbi. Razširjenost in popularnost družbenih omrežij na splošno in Twitterja konkretno spodbuja transformacije novinarskih postopkov. To vključuje vse faze: zbiranje, produkcijo in distribucijo, vključno s procesom selekcije novinarskih vsebin na podlagi novičarskih dejavnikov. Na področju selekcije novinarskih vsebin je obstajala raziskovalna vrzel pri proučevanju uporabe vsebin iz Twitterja v novinarskih prispevkih ter novičarskih dejavnikov, na podlagi katerih se uredniki odločajo glede tovrstne uporabe. V študiji smo na podlagi poglobljenih polstrukturiranih intervjujev z uredniki slovenskih medijev opredelili novičarske in druge kontekstualne dejavnike, na podlagi katerih se novinarji in uredniki odločajo, katere tvite bodo izbrali in jih na različne načine uporabili v prispevkih o volitvah v Evropski parlament leta 2014. Na podlagi analize izvedenih intervjujev lahko vzpostavimo naslednjo klasifikacijo novičarskih dejavnikov: elitne osebe, konfliktnost, zabava, Twitter kot tematika; hitrost oziroma aktualnost, dejavnik novičarske mreže, ekskluzivnost dostopa in Twitter kot medij; usmerjenost ter periodičnost medija. Strukturni vzorec kaže spremembe pri vlogi vsebinskih dejavnikov ter pomen produktnih, konkurenčnih in zunanjih dejavnikov.
Structure-Activity Relationships of Hainantoxin-IV and Structure Determination of Active and Inactive Sodium Channel Blockers*

Hainantoxin-IV (HNTX-IV) can specifically inhibit the neuronal tetrodotoxin-sensitive sodium channels and defines a new class of depressant spider toxin. The sequence of native HNTX-IV is ECLGFGKGCNPSNDQCCKSSNLVCSRKHRWCKYEI-NH2. In the present study, to obtain further insight into the primary and tertiary structural requirements of neuronal sodium channel blockers, we determined the solution structure of HNTX-IV as a typical inhibitor cystine knot motif and synthesized four mutants designed based on the predicted sites followed by structural elucidation of two inactive mutants. Pharmacological studies indicated that the S12A and R26A mutants had activities near that of native HNTX-IV, while K27A and R29A demonstrated activities reduced by 2 orders of magnitude. 1H MR analysis showed the similar molecular conformations for native HNTX-IV and four synthetic mutants. Furthermore, in the determined structures of K27A and R29A, the side chains of residues 27 and 29 were located in the identical spatial position to those of native HNTX-IV. These results suggested that residues Ser12, Arg26, Lys27, and Arg29 were not responsible for stabilizing the distinct conformation of HNTX-IV, but Lys27 and Arg29 were critical for the bioactivities. The potency reductions produced by Ala substitutions were primarily due to the direct interaction of the essential residues Lys27 and Arg29 with sodium channels rather than to a conformational change. After comparison of these structures and activities with correlated toxins, we hypothesized that residues Lys27, Arg29, His28, Lys32, Phe5, and Trp30 clustered on one face of HNTX-IV were responsible for ligand binding.
A Methodology and a Web Platform for the Collaborative Development of Context-Aware Systems

Information and services personalization is essential for an optimal user experience. Systems have to be able to acquire data about the user's context, process them in order to identify the user's situation and finally, adapt the functionality of the system to that situation, but the development of context-aware systems is complex. Data coming from distributed and heterogeneous sources have to be acquired, processed and managed. Several programming frameworks have been proposed in order to simplify the development of context-aware systems. These frameworks offer high-level application programming interfaces for programmers that complicate the involvement of domain experts in the development life-cycle. The participation of users that do not have programming skills but are experts in the application domain can speed up and improve the development process of these kinds of systems. Apart from that, there is a lack of methodologies to guide the development process. This article presents as main contributions, the implementation and evaluation of a web platform and a methodology to collaboratively develop context-aware systems by programmers and domain experts.
Representing Beliefs in a Situated Event Calculus 1 Motivation: Processing Car Crash Reports

This paper proposes an extension of the event calculus KS86] which allows the representation of alternative situations (states-of-aaairs) and beliefs. The basic idea of this situated event calculus is to use the notion of situations as developed in Situation Semantics, a linguistically motivated semantic theory BP83, BE87]. Instead of having events of the form`Happens(Action,Time)' all events occur relative to a speciic situation: `Happens(Action,Time,Sit)'. In other words, an event can happen in one situation and not happen in an otherwise similar situation. Situations can thus be viewed as collections of events and are used here to represent beliefs: a person adopting a situation has knowledge of all the events occurring in it and believes all the uents holding in it (ie all consequences of the events). Changing beliefs are modeled by adopting diierent situations. By using a circumscribed version of the event calculus Shanahan97] and modelingàdopt' and`believes' as ordinary events and uents, the frame problem is easily overcome, both wrt beliefs and \physical" uents. The motivation for the work presented in this paper stems from an application in Natural Language Processing, namely the automatic processing of car crash reports. These reports are short descriptions of accidents as found in statements for insurance companies. A corpus of 115 reports has been investigated by diierent research groups wrt various research issues relevant for NLP, such as syntactic and semantic phenomena, discourse structure, etc. This section brieey presents some sample texts containing explicit or implicit references to the driver's beliefs concerning the actual state-of-aaairs. One of these examples will be formally represented in our Situated Event Calculus in Section 4. The most simple accident reports only contain a description of the situation and an (unexpected) event which causes the accident. However, a substantial number of reports show a more complicated structure. Three types of such complicated structures recur frequently. In the rst one, the author describes not only the situation and an unexpected event but also his own unsuccessfull action to prevent the accident. Interestingly, such actions may be described indirectly. In the following text, though no explicit reference is made here to an action of braking in order to avoid the accident, the reader assumes that such an action has taken place. We were at Saint-Ouen, I was surprised when the person in front of me braked suddenly and, being unable to change lanes and the road being wet, I couldn't come to …
New clues on the calcium underabundance in early‐type galaxies

We use our new stellar population models, which include effects from variable element abundance ratios, to model the Ca4227 absorption line indices of early-type galaxies (Trager et al.), and to derive calcium element abundances. We find that calcium, although being an alpha-element, is depressed with respect to the other alpha-elements by up to a factor 2. This confirms quantitatively earlier speculations that early-type galaxies are calcium underabundant. We find a clear correlation between alpha/Ca ratio and central velocity dispersion, which implies that more massive galaxies are more calcium underabundant. Interestingly this correlation extends down to the dwarf spheroidal galaxies of the Local Group for which alpha/Ca ratios have been measured from high-resolution spectroscopy of individual stars (Shetrone et al.). The increase of the calcium underabundance with galaxy mass balances the higher total metallicities of more massive galaxies, so that calcium abundance in early-type galaxies is fairly constant and in particular does not increase with increasing galaxy mass. This result may be the key to understand why the CaII triplet absorption of early-type galaxies at 8600 A is constant to within 5 per cent over a large range of velocity dispersions (Saglia et al.; Cenarro et al.). The origin of the calcium underabundance in early-type galaxies remains yet to be understood. We argue that formation timescales are disfavoured to produce calcium underabundance, and that the option of metallicity dependent supernova yields may be the most promising track to follow
Quantum deformed magnon kinematics

The dispersion relation for planar = 4 supersymmetric Yang-Mills is identified with the Casimir of a quantum deformed two-dimensional kinematical symmetry, Eq(1, 1). The quantum deformed symmetry algebra is generated by the momentum, energy and boost, with deformation parameter q = e2πi/λ. Representing the boost as the infinitesimal generator for translations on the rapidity space leads to an elliptic uniformization with crossing transformations implemented through translations by the elliptic half-periods. This quantum deformed algebra can be interpreted as the kinematical symmetry of a discrete integrable model with lattice spacing given by the BMN length a = 2π/(λ)1/2. The interpretation of the boost generator as the corner transfer matrix is briefly discussed.
0.15µm BiC-DMOS technology with novel stepped-STI N-channel LDMOS

We developed a state-of-the-art BiC-DMOS process using 0. 15µm technology. High-voltage MOSFETs were embedded in our standard 0. 15µm CMOS process with a 0. 13µm high density NVM. More intelligent mixed signal devices can flexibly be realized by this technology. Moreover, the reliability of n-ch LDMOS is markedly improved by the novel structure of stepped-STI LDMOS.