Miracle-dz/UniFAR-FTUs huggingface dataset:
TripNet: A Method for Constructing Rooted Phylogenetic Networks from Rooted Triplets

The problem of constructing an optimal rooted phylogenetic network from an arbitrary set of rooted triplets is an NP-hard problem. In this paper, we present a heuristic algorithm called TripNet, which tries to construct a rooted phylogenetic network with the minimum number of reticulation nodes from an arbitrary set of rooted triplets. Despite of current methods that work for dense set of rooted triplets, a key innovation is the applicability of TripNet to non-dense set of rooted triplets. We prove some theorems to clarify the performance of the algorithm. To demonstrate the efficiency of TripNet, we compared TripNet with SIMPLISTIC. It is the only available software which has the ability to return some rooted phylogenetic network consistent with a given dense set of rooted triplets. But the results show that for complex networks with high levels, the SIMPLISTIC running time increased abruptly. However in all cases TripNet outputs an appropriate rooted phylogenetic network in an acceptable time. Also we tetsed TripNet on the Yeast data. The results show that Both TripNet and optimal networks have the same clustering and TripNet produced a level-3 network which contains only one more reticulation node than the optimal network.
Privacy-aware querying over sensitive trajectory data

Existing approaches for privacy-aware mobility data sharing aim at publishing an anonymized version of the mobility dataset, operating under the assumption that most of the information in the original dataset can be disclosed without causing any privacy violations. In this paper, we assume that the majority of the information that exists in the mobility dataset must remain private and the data has to stay in-house to the hosting organization. To facilitate privacy-aware sharing of the mobility data we develop a trajectory query engine that allows subscribed users to gain restricted access to the database to accomplish various analysis tasks. The proposed engine (i) audits queries for trajectory data to block potential attacks to user privacy, (ii) supports range, distance, and k-nearest neighbors spatial and spatiotemporal queries, and (iii) preserves user anonymity in answers to queries by (a) augmenting the real trajectories with a set of carefully crafted, realistic fake trajectories, and (b) ensuring that no user-specific sensitive locations are reported as part of the returned trajectories.
Verifying Interlevel Relations Within Multi-Agent Systems

An approach to handle the complex dynamics of a multi-agent system is based on distinguishing aggregation levels by structuring the system into parts or components. The behavior of every aggregation level is specified by a set of dynamic properties for components and interactions at that level, expressed in some (temporal) language. The dynamic properties of higher aggregation levels in principle can be logically related to dynamic properties of lower levels. This asks for identification and verification of such interlevel relations. In this article it is shown how this problem can be addressed using model checking techniques.
Rational families of vector bundles on curves, II

Let C be a smooth complex projective curve of genus at least 2 and let M be the moduli space of rank 2, stable vector bundles on C, with fixed determinant of degree 1. For any k>1, we find two irreducible components of the space of rational curves of degree k on M. One component, which we call the nice component has the property that the general element is a very free curve if k is sufficiently large. The other component has the general element a free curve. Both components have the expected dimension and their maximal rationally connected fibration is the Jacobian of the curve C.
Dipeptidyl Peptidase-4 Inhibitors Cause Bullous Pemphigoid in Diabetic Patients: Report of Two Cases

Bullous pemphigoid (BP) is an autoimmune disorder characterized by the production of autoantibodies against two antigens (BPAG1 and 2) and can be induced by drugs (1,2). Recently, the development of BP was reported in diabetic patients treated with dipeptidyl peptidase-4 inhibitors (gliptins) plus metformin (3). However, it remains unknown whether gliptins alone or in combination with metformin are responsible for the induction of BP. We report two diabetic patients who developed BP shortly after addition of vildagliptin to their metformin monotherapy. A 59-year-old woman and a 67-year- old man, both with type 2 diabetes that had been controlled with metformin for 6 and 3 years, respectively, presented with an 1- and 3-month history of pruritic …
In Vivo Monitoring of Inflammation After Cardiac and Cerebral Ischemia by Fluorine Magnetic Resonance Imaging

Background— In this study, we developed and validated a new approach for in vivo visualization of inflammatory processes by magnetic resonance imaging using biochemically inert nanoemulsions of perfluorocarbons (PFCs). Methods and Results— Local inflammation was provoked in 2 separate murine models of acute cardiac and cerebral ischemia, followed by intravenous injection of PFCs. Simultaneous acquisition of morphologically matching proton (1H) and fluorine (19F) images enabled an exact anatomic localization of PFCs after application. Repetitive 1H/19F magnetic resonance imaging at 9.4 T revealed a time-dependent infiltration of injected PFCs into the border zone of infarcted areas in both injury models, and histology demonstrated a colocalization of PFCs with cells of the monocyte/macrophage system. We regularly found the accumulation of PFCs in lymph nodes. Using rhodamine-labeled PFCs, we identified circulating monocytes/macrophages as the main cell fraction taking up injected nanoparticles. Conclusions— PFCs can serve as a “positive” contrast agent for the detection of inflammation by magnetic resonance imaging, permitting a spatial resolution close to the anatomic 1H image and an excellent degree of specificity resulting from the lack of any 19F background. Because PFCs are nontoxic, this approach may have a broad application in the imaging and diagnosis of numerous inflammatory disease states.
Effect of Sleeve Material on Interfacial Contact Behavior of CFRP-Metal Couples

A study was carried out on the contact pressure and shear stress at the interface of a carbon-fiber-reinforced polymer (CFRP) rod in contact with aluminum alloy or copper sleeves of different hardness. The main objective was to investigate the effect of the sleeve material on the interfacial sliding behavior under high contact pressures required for the design of wedge anchor systems to grip CFRP rods in prestressed concrete applications. The shear stress increased with the contact pressure; aluminum alloy sleeves generated higher shear stresses than copper sleeves. For both sleeve materials, higher shear stresses resulted from softening sleeves, an effect attributed to the lower yield stress facilitating metal flow, which resulted in a larger contact area between the sleeve and the CFRP rod.
Noncontact Mapping of the Heart: How and When to Use

Noncontact Mapping of the Heart. The noncontact mapping system is a new tool for electrophysiologic study and radiofrequency ablation. The mode of operation includes single beat, three‐dimensional, high‐density mapping. Careful analysis of unipolar electrograms and isopotential maps are essential to understand the mechanism of the arrhythmia. Radiofrequency catheter ablation guided by this system is effective in curing patients of their tachycardias.
Integration, modules, and development: molecules to morphology to evolution

coordinated and the end result is an integrated, functional organism. Similarly, there is considerable flexibility for evolutionary change of specific parts, while robustness of the overall body plan ensures continued integration of multiple organismal functions. Research in recent years has identified the modular architecture of organisms as one of the major principles that underlies this simultaneous flexibility and robustness (e.g., Raff 15
Uva-dare (digital Academic Repository) Surgery-induced Reactive Oxygen Species Enhance Colon Carcinoma Cell Binding by Disrupting the Liver Endothelial Cell Lining Surgery-induced Reactive Oxygen Species Enhance Colon Carcinoma Cell Binding by Disrupting the Liver Endothelial Cell Lining

(2011). Surgery-induced reactive oxygen species enhance colon carcinoma cell binding by disrupting the liver endothelial cell lining. General rights It is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s), other than for strictly personal, individual use, unless the work is under an open content license (like Creative Commons). Disclaimer/Complaints regulations If you believe that digital publication of certain material infringes any of your rights or (privacy) interests, please let the Library know, stating your reasons. In case of a legitimate complaint, the Library will make the material inaccessible and/or remove it from the website. Please Ask the Library: ABSTRACT Objective Resection of primary colorectal cancer is associated with enhanced risk of development of liver metastases. It was previously demonstrated that surgery initiated an early inflammatory response resulting in elevated tumour cell adhesion in the liver. Because reactive oxygen species (ROS) are shown to be produced and released during surgery, the effects of ROS on the liver vascular lining and tumour cell adhesion were investigated. Methods Human endothelial cell monolayers (human umbilical vein endothelial cells (HUVECs) and human microvascular endothelial cells of the lung (HMEC-1s)) were exposed to ROS production, after which electrical impedance, cellular integrity and tumour cell adhesion were investigated. Furthermore, surgery-induced tumour cell adhesion as well as the role of ROS and liver macrophages (Kupffer cells) in this process were studied in vivo. Results Production of ROS decreased cellular impedance of endothelial monolayers dramatically. Moreover, formation of intercellular gaps in endothelial monolayers was observed, exposing subendothelial extracellular matrix (ECM) on which colon carcinoma cells adhered via integrin molecules. Endothelial damage was, however, prevented in the presence of ROS-scavenging enzymes. Additionally, surgery induced downregulation of both rat and human liver tight junction molecules. Treatment of rats with the ROS scavenger edaravone prevented surgery-induced tumour cell adhesion and downregulation of tight junction proteins in the liver. Interestingly, depletion of Kupffer cells prior to surgery significantly reduced the numbers of adhered tumour cells and prevented disruption of expression of tight junction proteins. Conclusions In this study it is shown that surgery-induced ROS production by macrophages damages the vascular lining by downregulating tight junction proteins. This leads to exposure of ECM, to which circulating tumour cells bind. In light of this, perioperative therapeutic intervention, preventing surgery-induced inflammatory reactions, may reduce the risk of developing liver metastases, thereby improving …
An asymptotical method to estimate the parameters of a deteriorating system under condition-based maintenance

In this paper, we develop a new method to estimate the parameters of a deteriorating system under perfect condition-based maintenance. This method is based on the asymptotical behavior of the system, which is studied by using the renewal process theory. We obtain a Central Limit Theorem (CLT in the following) for the parameters. We compare the accuracy and the speed of the method with the maximum likelihood one (ML method in the following) on different examples.
Time-Delay-Domain and Pseudorandom-Noise Photoacoustic and Photothermal Wave Processes: A Review of the State of the Art

The application and development of correlation and spec- tral analysis methods to photoacoustic and photothermal wave detec- tion are examined. The purposes of this review are to 1) describe the two most prominent techniques available for photothermal correlation and spectral processing, namely the pseudorandom noise and the fre- quency-modulation (FM) time-delay (or frequency sweep) optical ex- citation; 2) compare the technical features of these techniques, such as measurement dynamic range properties, amount of measurement time required and instrumentation requirements; and 3) present advantages of the techniques over the widely used conventional frequency domain and pulsed laser excitation, as well as a detailed comparison between themselves. Attention is focused on the conceptual and mathematical details of signal generation, processing, and interpretation. Subtle but significant differences in the signal dynamic range, impulse response, and transfer function are shown to determine the limits of each of the two major techniques and are corroborated by the available experi- mental evidence to date. A review of the steadily increasing literature on spectroscopic and thermal imaging applications of these techniques is a powerful indicator of the promise they hold for conducting fun- damental and applied studies, primarily due to 1) the superior wealth of information obtained through pseudorandom photothermal exci- tation, as compared to the conventional frequency dispersive tech- niques and 2) the less destructive nature of the pseudorandom im- pulse response, compared to pulsed laser excitation.
Spoken Document Retrieval for TREC-9 at Cambridge University

This paper presents work done at Cambridge University for th e TREC-9 Spoken Document Retrieval (SDR) track. The CUHTK transcriptions from TREC-8 with Word Error Rate (WER) of 20.5% were used in conjunction with stopping, Porter stem ming, Okapi-style weighting and query expansion using a con temporaneous corpus of newswire. A windowing/recombinati on strategy was applied for the case where story boundaries wer e unknown (SU) obtaining a final result of 38.8% and 43.0% Average Precision for the TREC-9 short and terse queries respe ctively. The corresponding results for the story boundaries known runs (SK) were 49.5% and 51.9%. Document expansion was used in the SK runs and shown to also be beneficial for SU under certain circumstances. Non-lexical information was gener ated, which although not used within the evaluation, should prove useful to enrich the transcriptions in real-world applicat ons. Finally, cross recogniser experiments again showed there is l ittle performance degradation as WER increases and thus SDR now needs new challenges such as integration with video data.
Massive Hemoptysis: An Update on the Role of Bronchoscopy in Diagnosis and Management

Hemoptysis is frequently encountered in clinical practice, and may be the presenting symptom of a number of diseases. Although massive hemoptysis accounts for only 5–15% of episodes, it should always be considered as a life-threatening condition that warrants effective assessment and management. In this article, we review the literature with regard to the definition, etiology, epidemiology, pathophysiology, diagnosis and treatment of massive hemoptysis, with special emphasis on the role of bronchoscopy as a diagnostic and therapeutic tool. We briefly present the circumstances under which the use of rigid bronchoscopy should be preferred for controlling massive bleeding. Moreover, we address the crucial importance of multidisciplinary collaboration by illustrating the roles of endovascular therapy and surgery in the optimal management of massive hemoptysis.
(Ir)relevance of Gender? on the Influence of Gender Stereotypes on Learning with a Robot

Education research has documented a trend that reflects gender-based differences in the choice of fields of study. This, in turn, contributes to an imbalance in the representation of men and women in particular professions: In educational contexts, female teachers predominantly teach stereotypically female areas of study like social sciences and humanities, whereas male teachers are mainly represented in stereotypically male domains like mathematics. Research further provides evidence for the fact that this gender-stereotyped division of labor in education significantly impacts students' learning and motivation. Would gender-related stereotypes also bias learning processes with robots? This is plausible in light of the fact that social robots become more and more popular in learning settings. Thus, should the next generation of educational robots be ‘gendered’ and what impact would robot gender have on task performance, particularly in the context of a gender-stereotypical human-robot interaction (HRI) task? To investigate these issues, we examined the influence of robot gender on learning when completing either stereotypically female or stereotypically male learning tasks. 120 university students (60 females and 60 males) completed either stereotypically female or stereotypically male tasks with the support of a male vs. female instructor robot. The manipulation check indicated that participants recognized the robot's alleged gender correctly. Importantly, our results suggest that prevailing gender stereotypes associated with learning do not apply to robots that perform gender-stereotypical tasks. Interestingly, our findings indicated that a mismatch of robot gender and gender typicality of the respective task led to increased willingness to engage in prospective learning processes with the robot. We discuss these results with respect to future research on HRI and learning, and with regard to practical implications associated with the introduction of robots into higher education.
Population estimate and morphometry of ovarian preantral follicles from three recently recognized squirrel monkey species: a comparative study

Summary We describe morphological and morphometrical characteristics of preantral ovarian follicles from three recently recognized Saimiri species: S. macrodon, S. cassiquiarensis and S. vanzolinii; the last one a threatened species. Ovaries from four adult monkeys were evaluated: one pair from a pregnant S. macrodon, two ovarian pairs from S. cassiquiarensis females (one of them pregnant), and one left ovary from a senile S. vanzolinii, applying classical histology. Follicular preantral population was quantified and morphology and morphometry of primordial, primary and secondary follicles were evaluated. Follicular preantral population varied among species, being 347,153 in the ovaries of the S. macrodon, 270,342 and 278,376 in the ovaries of both adult non-pregnant and pregnant S. cassiquiarensis females, and 28,149 in the ovary from a senile S. vanzolinii. Most follicles were at primordial or transition stages, except for the senile S. vanzolinii female, which presented the lowest percentages of primordial and transition follicles when compared with primary and secondary ones. Most preantral follicles (>70%) were morphologically normal in the ovaries from all studied S. macrodon and S. cassiquiarensis females, but the ovary of the senile S. vanzolinii female presented a significant decrease in the percentage of normal follicles (primordial: 61%, transition: 52%, primary: 54%, and secondary: 48%). In general, follicular diameter increased significantly from primordial to transition, and subsequently from primary to secondary follicles.
Effect of acid in the duodenum on histamine-stimulated gastric secretion in man

EDITORIAL SYNOPSIS In normal subjects, the secretion of gastric juice in response to a constant intravenous infusion of histamine in near maximal dosage diminished when N/10 hydrochloric acid was infused into the proximal duodenum. In patients with duodenal ulcer the secretion of gastric juice was inhibited when submaximal doses of histamine were used but to a lesser degree than in the normal subjects. When the histamine stimulus was nearly maximal, no inhibition was found in the patients with duodenal ulcer.
Spatio-temporal instabilities of the Kirkendall marker planes during interdiffusion in β'-AuZn

Abstract A Kirkendall-effect-mediated behaviour (migration) of fiducial markers originally situated at the contact surface of a diffusion couple can be complex in both temporal and spatial domains. A phenomenological approach based on a concept of the Kirkendall velocity construction is used to rationalize the movement of the inert markers upon diffusion-controlled growth of the β'-AuZn intermetallic phase. It is demonstrated (experimentally as well as theoretically) that the Kirkendall marker planes can be multiple, stable or unstable within the single-phase reaction product. A general criterion of the microstructural instability of the Kirkendall plane is introduced.
SHEAR DESIGN OF HIGH- AND NORMAL STRENGTH CONCRETE BEAMS WITH WEB REINFORCEMENT

This work examines 14 beams with stirrups failing in shear, in addition to 107 from the literature. These include high-strength (HSC) beams and normal strength concrete (NSC) beams. It is shown that using ACI Building Code Equation for concrete contribution is conservative for both HSC and NSC over a wide range of the pricipal variables; concrete compressive strength; stirrup nominal strength; longitudinal steel ratio; and shear span-to-depth ratio. However, a higher coefficient of variation (COV) is obtained using the more conservative Canadian code simple design alternative. A proposed design method is also discussed that is conservative with a lower COV than the ACI Equation.
Parthenogenetic activation of bovine oocytes using single and combined strontium, ionomycin and 6-dimethylaminopurine treatments

Summary In vitro-matured (IVM) bovine oocytes were activated with single and combined treatments of strontium (S), ionomycin (I) and 6-DMAP (D). Using oocytes IVM for 26 h, we observed that activation altered cell cycle kinetics (faster progression, MIII arrest, or direct transition from MII to pronuclear stage) when compared to in vitro fertilization. The effect of oocyte age on early parthenogenesis was assessed in oocytes IVM for 22, 26 and 30 h. Better results in pronuclear development were obtained in treatments ISD (81.7%) at 22 h; D (66.7%), IS (63.3%), ID (73.3%) and ISD (76.7%) at 26 h; and D (86.7%), IS (85.0%) and ID (78.3%) at 30 h. Higher cleavage occurred on ISD (80.0%) at 22 h; ID (83.3%) and ISD (91.7%) at 26 h; and I (86.7%), IS (90.0%), ID (85.0%) and ISD (95.0%) at 30 h. More blastocysts were achieved in ID (25.0%) and ISD (18.3%) at 22 h; and in ID at 26 h (45.0%) and 30 h (50.0%). We also observed that IS allowed higher haploid (77.4%) embryonic development, whilst ID was better for diploid (89.1%) development. It was concluded that association of S and D without I was not effective for blastocyst development; treatments using S were less influenced by oocyte age, but when S was associated with D there was a detrimental effect on aged oocytes; treatment ISD promoted higher activation and cleavage rates in young oocytes and ID protocol was the best for producing blastocysts.