Miracle-dz/UniFAR-FTUs huggingface dataset:
Pathogenic Forms of Tau Inhibit Kinesin-Dependent Axonal Transport through a Mechanism Involving Activation of Axonal Phosphotransferases

Aggregated filamentous forms of hyperphosphorylated tau (a microtubule-associated protein) represent pathological hallmarks of Alzheimer's disease (AD) and other tauopathies. While axonal transport dysfunction is thought to represent a primary pathogenic factor in AD and other neurodegenerative diseases, the direct molecular link between pathogenic forms of tau and deficits in axonal transport remain unclear. Recently, we demonstrated that filamentous, but not soluble, forms of wild-type tau inhibit anterograde, kinesin-based fast axonal transport (FAT) by activating axonal protein phosphatase 1 (PP1) and glycogen synthase kinase 3 (GSK3), independent of microtubule binding. Here, we demonstrate that amino acids 2–18 of tau, comprising a phosphatase-activating domain (PAD), are necessary and sufficient for activation of this pathway in axoplasms isolated from squid giant axons. Various pathogenic forms of tau displaying increased exposure of PAD inhibited anterograde FAT in squid axoplasm. Importantly, immunohistochemical studies using a novel PAD-specific monoclonal antibody in human postmortem tissue indicated that increased PAD exposure represents an early pathogenic event in AD that closely associates in time with AT8 immunoreactivity, an early marker of pathological tau. We propose a model of pathogenesis in which disease-associated changes in tau conformation lead to increased exposure of PAD, activation of PP1-GSK3, and inhibition of FAT. Results from these studies reveal a novel role for tau in modulating axonal phosphotransferases and provide a molecular basis for a toxic gain-of-function associated with pathogenic forms of tau.
Counterparty Risk on Interest Rate Derivatives in a Multiple Curve Setup

We study the valuation and hedging of CSA interest rate derivatives. By CSA interest rate derivatives, we mean a portfolio of OTC interest rate derivatives between two defaultable counterparties, connected by the means of a netting agreement regarding the counterparty risk related cash flows between the two parties. CSA cash flows comprise the collateral relative to this netted set of contracts, and the close-out cash flows in case of default of either party. The first step consists in studying the so-called counterparty clean valuation of the portfolio, namely the valuation in a hypothetical situation where the parties would be risk-free, yet accounting for the post-crisis discrepancy between the risk-free discount curve, and the LIBOR fixing curve. Toward this view we resort to a defaultable HJM methodology, in which this discrepancy is accounted for by the possibility of a stylized default of the LIBOR contributing banks, which would be priced by the market. Specific short rate examples are given in the form of an extended CIR and a Lévy Hull–White model for the risk-free short rate and the LIBOR short credit spread. In the second step, the counterparty clean value process of the portfolio is used as an underlier to an option, which prices the correction in value (CVA) to the portfolio due to the counterparty risk, in accordance with the corresponding CSA. The post-crisis multiple curve issue (including the above discrepancy) implies that the CVA should also account for the costs of funding a position in the portfolio and in its collateral, and of setting-up a related hedge. We model funding costs in the form of liquidity bases. We then develop a reduced-form, pre-default, backward stochastic differential equations (BSDE) approach to the problem of pricing and hedging interest rate counterparty risk. The problem of pricing and hedging interest rate counterparty risk, can thus reduced to low-dimensional Markovian pre-default CVA BSDEs, or equivalent semi-linear PDEs.
Hepatotoxicity in Guinea Pigs Following Acute Inhalation Exposure to 1,1-Dichloro-2,2,2-Trifluoroethane

Groups of 10 male Hartley guinea pigs were exposed to 3.0, 2.0, 1.0, or 0.1% (v/v) 1,1-Dichloro-2,2,2-trifluoroethane (HCFC-123) or 1.0% (v/v) halothane by inhalation for 4 hr. A sixth group of 10 guinea pigs received only air. All animals were sacrificed 48 hr postexposure. Gross and histopathologic examination of the liver, heart, and kidney and routine hematology and clinical chemistry analyses [including isocitrate dehydrogenase (ICDH)] were done on all guinea pigs. Lesions related to HCFC-123 and halothane exposure were limited to the liver and included centrolobular vacuolar (fatty) change, multifocal random degeneration and necrosis, and centrolobular degeneration and necrosis. These lesions were observed in 90-100% of the exposed animals and were absent in the air-only controls. There was significant individual animal variation in susceptibility to both HCFC-123 and halothane, resulting in a spectrum of histologic lesions and clinical chemistry values within each exposure group. Alanine aminotransferase, aspartate aminotransferase, and ICDH were the most significant predictors of hepatocellular damage. Similarities in the response between halothane and HCFC-123 in this guinea pig model suggests that humans susceptible to halothane-induced hepatitis may be susceptible to HCFC-123 by a common mechanism of toxicity.
Animals Versus Animats: Or Why Not Model the Real Iguana?

The overlapping fields of adaptive behavior and artificial life are often described as novel approaches to biology. They focus attention on bottom-up explanations and how lifelike phenomena can result from relatively simple systems interacting dynamically with their environments. They are also characterized by the use of synthetic methodologies, that is, building artificial systems as a means of exploring these ideas. Two differing approaches can be distinguished: building models of specific animal systems and assessing them within complete behavior—environment loops; and exploring the behavior of invented artificial animals, often called animats, under similar conditions. An obvious question about the latter approach is, how can we learn about real biology from simulation of non-existent animals? In this article I will argue, first, that animat research, to the extent that it is relevant to biology, should also be considered as model building. Animat simulations do, implicitly, represent hypotheses about, and should be evaluated by comparison to, animals. Casting this research in terms of invented agents serves only to limit the ability to draw useful conclusions from it by deflecting or deferring any serious comparisons of the model mechanisms and results with real biological systems. Claims that animat models are meant to be existence proofs, idealizations, or represent general problems in biology do not make these models qualitatively different from more conventional models of specific animals, nor undermine the ultimate requirement to justify this work by making concrete comparisons with empirical data. It is thus suggested that we will learn more by choosing real, and not made-up, targets for our models.
New SigD-regulated genes identified in the rhizobacterium Bacillus amyloliquefaciens FZB42

ABSTRACT The alternative sigma factor D is known to be involved in at least three biological processes in Bacilli: flagellin synthesis, methyl-accepting chemotaxis and autolysin synthesis. Although many Bacillus genes have been identified as SigD regulon, the list may be not be complete. With microarray-based systemic screening, we found a set of genes downregulated in the sigD knockout mutant of the plant growth-promoting rhizobacterium B. amyloliquefaciens subsp. plantarum FZB42. Eight genes (appA, blsA, dhaS, spoVG, yqgA, RBAM_004640, RBAM_018080 and ytk) were further confirmed by quantitative PCR and/or northern blot to be controlled by SigD at the transcriptional level. These genes are hitherto not reported to be controlled by SigD. Among them, four genes are of unknown function and two genes (RBAM_004640 and RBAM_018080), absent in the model strain B. subtilis 168, are unique to B. amyloliquefaciens stains. The eight genes are involved in sporulation, biofilm formation, metabolite transport and several other functions. These findings extend our knowledge of the regulatory network governed by SigD in Bacillus and will further help to decipher the roles of the genes. Summary: New SigD-regulated genes were identified in the plant growth-promoting rhizobacterium Bacillus amyloliquefaciens FZB42, which is closely related to the model organism B. subtilis.
Unmanaged Internet Protocol

Though appropriate for core Internet infrastructure, the Internet Protocol is unsuited to routing within and between emerging ad-hoc edge networks due to its dependence on hierarchical, administratively assigned addresses. Existing ad-hoc routing protocols address the management problem but do not scale to Internet-wide networks. The promise of ubiquitous network computing cannot be fulfilled until we develop an Unmanaged Internet Protocol (UIP), a scalable routing protocol that manages itself automatically. UIP must route within and between constantly changing edge networks potentially containing millions or billions of nodes, and must still function within edge networks disconnected from the main Internet, all without imposing the administrative burden of hierarchical address assignment. Such a protocol appears challenging but feasible. We propose an architecture based on self-certifying, cryptographic node identifies and a routing algorithm adapted from distributed hash tables.
ICDAR 2013 Competition on Writer Identification

Writer identification is important for forensic analysis, helping experts to deliberate on the authenticity of documents. The ICDAR2013 Competition on Writer Identification is part of a competition series (see also ICDAR2011 and ICFHR2012 Writer Identification Contests) which is dedicated to record recent advances in the field of writer identification for Latin scripts using established evaluation performance measures. The benchmarking dataset was created with the help of 250 writers that were asked to copy four parts of text in two Latin based languages (English and Greek). This paper describes the contest details including the evaluation measures used as well as the performance of the 12 submitted methods by 6 different groups along with a short description of each method.
Raman spectrum of carbonaceous material: a possible metamorphic grade indicator for low‐grade metamorphic rocks

Raman spectral analyses of carbonaceous material (CM) extracted from pelitic samples along two sections traversing the metamorphic belt of Taiwan were carried out in the present study. The results show similar spectral variations of CM with metamorphic grade as those documented in the literature. However, continuous sampling from zeolite facies through prehnite–pumpellyite facies to greenschist facies metamorphic rocks in the present study does reveal some interesting features on the Raman spectra of CM that were not noted before. Both the Raman D (disordered-)/O (ordered-) peak area (i.e. integrated intensity) ratio and the D/O peak width (i.e. full width at half maximum, FWHM) ratio of the CM decrease with progressive metamorphism, but the most prominent change in the D/O peak area ratio occurs in samples of lower greenschist facies metamorphic grade, while the most significant decrease in the D/O peak width ratio occurs in samples near the boundary of prehnite–pumpellyite facies and greenschist facies. This phenomenon is interpreted as a result of the decoupling of the changing rates of in-plane crystallite size and degree of defects of CM with progressive metamorphism. It is postulated that the Raman spectrum of CM can serve as a metamorphic grade indicator to distinguish samples of prehnite–pumpellyite facies metamorphic grade from those of greenschist facies metamorphic grade.
The Measure of cosmological parameters

A method for increasing the recovery of oil from a subterranean formation having at least one producer wellbore drilled therein, whereby a generally horizontal and generally circular wellbore is drilled so that oil is located between the generally horizontal and generally circular wellbore and the at least one producer wellbore. Fluid is injected through the generally horizontal and generally circular wellbore into the formation so that oil is swept to the at least one producer wellbore for recovery through the at least one producer wellbore.
Sorafenib for the treatment of recurrent hepatocellular carcinoma after liver transplantation: does mTOR inhibitors association augment toxicity?

potential limitation of this study is that it has only a small number of BCS patients enrolled prospectively during a 6-month period, which might require external validity. Certainly, it is often difficult to obtain a larger sample size from a single center during a relatively short period, given the rarity of this disease. Ideally, a nationwide epidemiological study should be carried out to evaluate the prevalence of thrombotic risk factors in Chinese BCS patients.
The experimental basis for interpreting particle and magnetic fabrics of sheared till

Particle fabrics of basal tills may allow testing of the bed‐deformation model of glacier flow, which requires high bed shear strains (>100). Field studies, however, have not yielded a systematic relationship between shear‐strain magnitude and fabric development. To isolate this relationship four basal tills and viscous putty were sheared in a ring‐shear device to strains as high as 714. Fabric was characterized within a zone of shear deformation using the long‐axis orientations of fine‐gravel and sand particles and the anisotropy of magnetic susceptibility (AMS) of small (∼5·8 cm3) intact samples. Results indicate that till particles rotate toward the plane of shearing with long‐axis orientations that become tightly clustered in the direction of shear (0·78 < S1 < 0·94 for three‐dimensional data). These strong, steady‐state fabrics are attained at shear strains of 7–30, with no evidence of fabric weakening with further strain, regardless of the specific till or particle‐size fraction under consideration. These results do not support the Jeffery model of particle rotation, which correctly describes particle rotation in the viscous putty but not in the tills, owing to fluid‐mechanical assumptions of the model that are violated in till. The sensitivity of fabric development to shear‐strain magnitude indicates that, for most till units where shear‐strain magnitude is poorly known, attributing fabric variations to spatial differences in other variables, such as till thickness or water content, will be inherently speculative. Attributing fabric characteristics to particular basal till facies is uncertain because shear‐strain magnitude is unlikely to be closely correlated to till facies. Weak or spatially variable fabrics, in the absence of post‐depositional disturbance or major deviations from unidirectional simple shear, indicate that till has not been pervasively sheared to the high strains required by the bed‐deformation model. Strong flow‐parallel fabrics are a necessary but insufficient criterion for confirming the model. Copyright © 2008 John Wiley & Sons, Ltd.
A Hierarchical Model of Binocular Rivalry

Binocular rivalry is the alternating percept that can result when the two eyes see different scenes. Recent psychophysical evidence supports the notion that some aspects of binocular rivalry bear functional similarities to other bistable percepts. We build a model based on the hypothesis (Logothetis & Schall, 1989; Leopold & Logothetis, 1996; Logothetis, Leopold, & Sheinberg, 1996) that alternation can be generated by competition between top-down cortical explanations for the inputs, rather than by direct competition between the inputs. Recent neurophysiological evidence shows that some binocular neurons are modulated with the changing percept; others are not, even if they are selective between the stimuli presented to the eyes. We extend our model to a hierarchy to address these effects.
Research on Chord algorithm based on polycyclic structure

In order to improve the searching efficiency of the classical Chord algorithm which is applied to the second generation of P2P network, we studied the Chord algorithm based on the polycyclic structure. Combining the multi-ring structure with group structure, polycyclic Chord algorithm links the whole nodes into multiple rings with recursive algorithm and uses active node in one group to record all routing information of the groups. In this paper, a new approach of entry of traditional routing table was proposed and a new description of successor node using grouping ideas was made which can reduce the amount of redundant information. Analysis shows that the Polycyclic Chord algorithm gains clear advantage over the original Chord algorithm in the terms of time complexity. Meanwhile, since the grouping strategy was involved in the new algorithm, a preliminary study about the grouping parameter k was also made in order to improve the effectiveness and efficiency of query. Finally, experimental results showed that the Polycyclic Chord algorithm can effectively reduce the average query hop while maintaining the other performance of the chord algorithm.
Representing concerns in source code

A software modification task often addresses several concerns. A concern is anything a stakeholder may want to consider as a conceptual unit, including features, nonfunctional requirements, and design idioms. In many cases, the source code implementing a concern is not encapsulated in a single programming language module, and is instead scattered and tangled throughout a system. Inadequate separation of concerns increases the difficulty of evolving software in a correct and cost-effective manner. To make it easier to modify concerns that are not well modularized, we propose an approach in which the implementation of concerns is documented in artifacts, called concern graphs. Concern graphs are abstract models that describe which parts of the source code are relevant to different concerns. We present a formal model for concern graphs and the tool support we developed to enable software developers to create and use concern graphs during software evolution tasks. We report on five empirical studies, providing evidence that concern graphs support views and operations that facilitate the task of modifying the code implementing scattered concerns, are cost-effective to create and use, and robust enough to be used with different versions of a software system.
Comparative analysis of microsatellite and allozyme markers: a case study investigating microgeographic differentiation in brown trout (Salmo trutta)

A comparative study between microsatellite and allozyme markers was conducted on natural populations of resident brown trout (Salmo trutta) sampled over a reduced geographical scale and on hatchery strains. The higher level of polymorphism observed at microsatellite loci resulted in higher power of statistical tests for differentiation among population samples and for genotypic linkage disequilibrium. Genetic distances of Cavalli-Sforza and Edwards were on average two times larger for microsatellites than for allozymes but multilocus FST estimates computed over the entire set of populations were not significantly different for both categories of markers. Assignment tests of individual fish to the set of sampled populations demonstrated a much higher efficiency of microsatellites compared to allozymes. Pairwise multilocus FST estimates were significantly correlated to waterway distances and there was a significant tendency for the incorrectly classified individuals to be assigned to one of the nearest populations, indicating that isolation-by-distance acted significantly on brown trout populations. This increase of differentiation with distance was higher for allozymes than for microsatellites. Traditional measures of genetic differentiation (Cavalli-Sforza and Edwards' chord distance and FST) were compared for microsatellites to recently proposed statistics taking into account allele size differences (Goldstein's distance and PST). Using Goldstein's distance for neighbour-joining analysis did not improve the tree structure resolution. Multilocus estimates of PST and FST were not significantly different when computed over the entire set of populations but no significant correlation was detected between matrices of pairwise multilocus PST estimates and waterway distances.
Tracking and identifying burglar using collaborative sensor-camera networks

This work presents BurTrap, a networking system which integrates wireless modules (such as TelosB nodes) with networked surveillance cameras to automatically, accurately, timely track and identify burglar who stole the property. First, we design an energy-efficient wakeup scheduling protocol that guarantees a successful target tracking while reducing the communication energy consumption of the portable wireless module. Then, we identify burglar among all the objects appeared in the obtained video information by performing trajectory fitting between the estimated geometric trajectory and the estimated local visual trajectory. Through extensive experiments, we show that BurTrap can pinpoint the burglar with extremely high accuracy.
A relay node selection technique for opportunistic routing in mobile Ad Hoc networks

In this paper, we propose a new relay node selection algorithm: relay node selection Considering Future Path(CFP) for opportunistic routings in mobile Ad Hoc networks, aiming to provide enhanced performance of successful delivery ratio. CFP based on the shortest distance algorithm and it not only considers the current distance towards the destination but also considers the future hops and estimates whether through the current node can a packet arrive at the destination. CFP can enhance the performance of successful delivery ratio by solving the potential problem of no forwarding relays in the shortest distance algorithm. Simulation results show that contrast against the shortest distance algorithm in opportunistic routing protocol GeRaF, CFP has better performance on both delivery ratio and goodput.
Risk of Ischemic Stroke Associated with the Use of Antipsychotic Drugs in Elderly Patients: A Retrospective Cohort Study in Korea

Objective Strong concerns have been raised about whether the risk of ischemic stroke differs between conventional antipsychotics (CAPs) and atypical antipsychotics (AAPs). This study compared the risk of ischemic stroke in elderly patients taking CAPs and AAPs. Method We conducted a retrospective cohort study of 71,584 elderly patients who were newly prescribed the CAPs (haloperidol or chlorpromazine) and those prescribed the AAPs (risperidone, quetiapine, or olanzapine). We used the National Claims Database from the Health Insurance Review and Assessment Service (HIRA) from January 1, 2006 to December 31, 2009. Incident cases for ischemic stroke (ICD-10, I63) were identified. The hazard ratios (HR) for AAPs, CAPs, and for each antipsychotic were calculated using multivariable Cox regression models, with risperidone as a reference. Results Among a total of 71,584 patients, 24,668 patients were on risperidone, 15,860 patients on quetiapine, 3,888 patients on olanzapine, 19,564 patients on haloperidol, and 7,604 patients on chlorpromazine. A substantially higher risk was observed with chlorpromazine (HR = 3.47, 95% CI, 1.97–5.38), which was followed by haloperidol (HR = 2.43, 95% CI, 1.18–3.14), quetiapine (HR = 1.23, 95% CI, 0.78–2.12), and olanzapine (HR = 1.12, 95% CI, 0.59–2.75). Patients who were prescribed chlorpromazine for longer than 150 days showed a higher risk (HR = 3.60, 95% CI, 1.83–6.02) than those who took it for a shorter period of time. Conclusions A much greater risk of ischemic stroke was observed in patients who used chlorpromazine and haloperidol compared to risperidone. The evidence suggested that there is a strong need to exercise caution while prescribing these agents to the elderly in light of severe adverse events with atypical antipsychotics.