Miracle-dz/UniFAR-FTUs huggingface dataset:
Catching the phylogenic history through the ontogenic hourglass: a phylogenomic analysis of Drosophila body segmentation genes

SUMMARY The phylogenetic information content of different developmental stages is a long‐standing issue in the study of development and evolution. We performed phylogenetic analyses of 51 body segmentation genes in 12 species of Drosophila in order to investigate the impact of the mode of evolution of development on phylogeny inference. Previous studies of these genes in Drosophila using pairwise phenetic comparisons at the species group level revealed the presence of an “hourglass model” (HG), wherein mid‐embryonic stages are the most evolutionarily constrained. We utilized two character‐based approaches: taxonomic congruence using the relative consensus fork index (RCFI), in which phylogenies are inferred from each gene separately and compared with a total evidence tree (TET), and partitioned simultaneous analysis using several indices such as branch support (BS) and localized incongruence length difference (LILD) test. We also proposed a new index, the recapitulatory index (R), which divides the number of synapomorphies on the total number of informative characters in a data set. Polynomial adjustment of both BS and R indices showed strong support for the hourglass model regardless of the taxonomic level (species subgroup vs. subgenera), showing less phylogenetic information content for mid‐developmental stages (mainly the zygotic segment polarity stage). Significant LILD scores were randomly distributed among developmental stages revealing the absence of differential selective constraints, but were significantly related to chromosomal location showing physical (linkage) impact on phylogenetic incongruence. RCFI was the most sensitive measure to taxonomic level, having a convex parabola at the species subgroup level in support of the hourglass model and a concave parabola at the subgeneric level in support of the adaptive penetrance model. This time‐dependent discrepancy of best fit developmental model parallels previous conflicting results from the vertebrates. Because of the quasi‐phenetic nature of this index, we argue that the discrepancy is due to the evolutionary rate heterogeneity of developmental genes rather than to fundamental differences among organisms. We suggest that simultaneous character‐based analyses give better macroevolutionary support to the hourglass model of the developmental constraints on genome evolution than pairwise phenetic comparisons.
Gene Expression Profiling of Human Stent-Induced Neointima by cDNA Array Analysis of Microscopic Specimens Retrieved by Helix Cutter Atherectomy: Detection of FK506-Binding Protein 12 Upregulation

Background —Restenosis due to neointima formation is the major limitation of stent-supported balloon angioplasty. Despite abundant animal data, molecular mechanisms of neointima formation have been investigated on only a limited basis in patients. This study sought to establish a method for profiling gene expression in human in-stent neointima and to identify differentially expressed genes that may serve as novel therapeutic targets. Methods and Results —We retrieved tissue specimens from patients with symptomatic in-stent restenosis using a novel helix cutter atherectomy device. cDNA samples prepared from neointima (n=10) and, as a control, from the media of normal arteries (n=14) were amplified using a novel polymerase chain reaction protocol and hybridized to cDNA arrays. Immunohistochemistry characterized the atherectomy material as neointima. cDNA arrays readily identified differentially expressed genes. Some of the differentially expressed genes complied with expected gene expression patterns of neointima, including downregulation of desmin and upregulation of thrombospondin-1, cyclooxygenase-1, and the 70-kDa heat shock protein B. Additionally, we discovered previously unknown gene expression patterns, such as downregulation of mammary-derived growth inhibitor and upregulation of FK506-binding protein 12 (FKBP12). Upregulation of FKBP12 was confirmed at the protein level in neointimal smooth muscle cells. Conclusions —Gene expression patterns of human neointima retrieved by helix-cutter atherectomy can be reliably analyzed by cDNA array technology. This technique can identify therapeutic targets in patients, as exemplified by the findings regarding FKBP12. FKBP12 is the receptor for Rapamycin (sirolimus), which in animal models reduced neointima formation. Our study thus yields a rationale for the use of Rapamycin to prevent restenosis in patients.
Detection of failing sensors by conflicting evidence in Bayesian classification

Classification has various applications, e.g., technical monitoring, medical diagnosis, financial scoring, and pattern recognition. In a classification problem, a class out of finitely many has to be chosen on basis of observed feature values. Bayesian Networks and particularly Naı̈ve Bayes Networks are an established approach to classification, where evidence from different sources is fused into a classification result. Sometimes pieces of evidence from different sources provide substantially different but reliable information, called conflicts. This paper proposes an approach to use conflicting evidence for performing diagnostic failure-tests of technical sources in Bayesian classification processes. Two approaches, called Conflict Ratio FailureTest and Conflict Binomial Failure-Test are described. Based on an air surveillance scenario, a simulation is used to provide a proof of concept and to compare these two diagnostic failure-test approaches.
Behavioral Pharmacology of Human Drug Dependence

Abstract : A review of the contributions of research on behavioral mechanisms of drug dependence, to interpret the relation of animal and human behavioral pharmacology findings to prevention of human drug dependence. The monograph brings together concepts from clinical and behavioral pharmacology and seeks the common processes underlying various forms of substance abuse. It describes effects of personality and the individual's history of drug exposure upon drug self-administration and discusses control of drug-related behavior by external and internal stimuli. Other sections deal with commonalities and differences among reinforcers and the maintenance of drug dependence by complex second-order schedules, in which drug-using behavior is maintained by environmental stimuli only remotely linked with drug administration. Keywords: Drug addiction, Pharmacology, Conditioned responses, Conditioned stimulus, Substances abuse, Behavior, Self-administration of drugs.
Prognostics Health Monitoring (PHM) for Prior-Damage Assessment in Electronics Equipment under Thermo-Mechanical Loads

Methodologies for prognostication and health monitoring can significantly impact electronic reliability for applications in which even minimal risk of failure may be unbearable. Prognostics health-monitoring (PHM) approach presented in this paper is different from state-of-art diagnostics and resides in the pre-failure-space of the electronic-system, in which no macro-indicators such as cracks or delamination exist. The presented PHM methodologies enable the estimation of prior damage in deployed electronics by interrogation of the system state. The presented methodologies will trigger repair or replacement, significantly prior to failure. The approach involves the use of condition monitoring devices which can be interrogated for damage proxies at finite time-intervals. The system's residual life is computed based on residual-life computation algorithms. In this paper a mathematical approach has been presented to calculate the prior damage in electronics subjected to cyclic and isothermal thermo-mechanical loads. Electronic components operating in a harsh environment may be subjected to both temperature variations in addition to thermal aging during use-life. Data has been collected for leading indicators of failure for 95.5Sn4Ag0. 5Cu first-level interconnects under both single and sequential application of cyclic and isothermal thermo-mechanical loads. Methodology for the determination of prior damage history has been presented using non-linear least-squares method based interrogation techniques. The methodology presented used the Levenberg-Marquardt Algorithm. Test vehicle includes various area-array packaging architectures soldered on Immersion Ag finish, subjected to thermal cycling in the range of -40degC to 125degC and isothermal aging at 125degC.
Explicit action perception shares resources with music syntax: A controlled behavioral study

A Controlled Behavioral Study Eleanor Harding1, Daniela Sammler2, Alessandro D’Ausilio3, Angela Friederici2, Luciano Fadiga3, 4, & Stefan Koelsch5 1 Minerva Research Group "Neurocognition of Rhythm in Communication," Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany 2 Department of Neuropsychology, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany 3 Italian Institute of Technology, Genoa, Italy – 4 University of Ferrara, DSBTA – Section of Human Physiology, Ferrara, Italy 5 Freie Universitat Berlin, Cluster of Excellence “Languages of Emotion”, Berlin, Germany
Responsibility for Homework: Children's Ideas about Self-Regulation.

Responsibility, it has been argued, can be usefully studied if it is defined in terms of specific principles, such as self-regulation. This study investigated children's practices and ideas about self-regulation for two particular aspects of schoolwork, namely, completing homework and learning for a class test. The material presented was from a sample of 86 Anglo children (30 7-year-olds, 26 9-year-olds, 30 11-year-olds). Children were interviewed individually, asked about practices and given vignettes which tapped ideas about self-regulation. Results indicated few age differences in practices, but an age-related shift in ideas, from otherregulation (7-year-olds) to self-regulation (11-yearolds). Findings are discussed in terms of the link between responsible practice and the development of understanding of the implications of self-regulation.
Does Using a Chair Backrest or Reducing Seated Hip Flexion Influence Trunk Muscle Activity and Discomfort? A Systematic Review

Objective: This paper systematically reviews the effect of chair backrests and reducing seated hip flexion on low back discomfort (LBD) and trunk muscle activation. Background: Prolonged sitting commonly exacerbates low back pain (LBP). Several modifications to seated posture and chair design have been recommended, including using chairs with backrests and chairs that reduce hip flexion. Method: Electronic databases were searched by two independent assessors. Part 1 of this review includes 26 studies comparing the effect of sitting with at least two different hip angles. In Part 2, seven studies that compared the effect of sitting with and without a backrest were eligible. Study quality was assessed using the PEDro scale. Results: Significant confounding variables and a relatively small number of randomized controlled trials (RCTs) involving people with LBP complicates analysis of the results. There was moderate evidence that chair backrests reduce paraspinal muscle activation, and limited evidence that chair backrests reduce LBD. There was no evidence that chairs involving less hip flexion reduce LBP or LBD, or consistently alter trunk muscle activation. However, participants in several studies subjectively preferred the modified chairs involving less hip flexion. Conclusion: The limited evidence to support the use of chairs involving less seated hip flexion, or the effect of a backrest, is consistent with the limited evidence that other isolated chair design features can reduce LBP. Application: LBP management is likely to require consideration of several factors in addition to sitting position. Larger RCTs involving people with LBP are required.
Increased migration and metastatic potential of tumor cells expressing aquaporin water channels

Aquaporin (AQP) water channels are expressed in high‐grade tumor cells of different tissue origins. Based on the involvement of AQPs in angiogenesis and cell migration, we tested whether AQP expression in tumor cells might enhance their migration and metastatic potential. Transfection of B16F10 and 4T1 tumor cells with AQP1 did not affect their appearance, size, growth, or substrate adherence but increased their plasma membrane osmotic water permeability by 5‐ to 10‐fold. In vitro analysis of cell migration by transwell assay, wound healing and video microscopy showed a 2‐ to 3‐fold accelerated migration of the AQP1‐expressing tumor cells compared to control cells. In mice, AQP1 expression increased tumor cell extravasation by > 1.5‐fold as quantified by counting tumor cells in lung at 6 h after tail vein injection of a mixture of fluorescently tagged AQP1‐expressing and control tumor cells. AQP1 expression also increased by 3‐fold the number of lung metastases 14 days after tail vein injection of tumor cells, with alveolar wall infiltration seen with AQP1‐expressing tumor cells. Our results provide evidence for AQP‐facilitated tumor cell migration and spread, suggesting a novel function for AQP expression in high‐grade tumors. AQP inhibition may thus reduce the metastatic potential of some tumors. —Hu, J., Verkman, A. S. Increased migration and metastatic potential of tumor cells expressing aquaporin water channels. FASEB J. 20, 1228–1236 (2006)
Sub-arcsec imaging of the AB Aur molecular disk and envelope at millimeter wavelengths: a non Keplerian disk

We present sub-arcsecond images of AB Auriga obtained with the IRAM Plateau de Bure interferometer in the isotopologues of CO, and in continuum at 3 and 1.3 mm. Instead of being centrally peaked, the continuum emission is dominated by a bright, asymmetric (spiral-like) feature at about 140 AU from the central star. The large scale molecular structure suggests the AB Aur disk is inclined between 23 and 43 degrees, but the strong asymmetry of the continuum and molecular emission prevents an accurate determination of the inclination of the inner parts. We find significant non-Keplerian motion, with a best fit exponent for the rotation velocity law of 0.41 +/- 0.01, but no evidence for radial motions. The disk has an inner hole about 70 AU in radius. The disk is warm and shows no evidence of depletion of CO. The dust properties suggest the dust is less evolved than in typical T Tauri disks. Both the spiral-like feature and the departure from purely Keplerian motions indicates the AB Aur disk is not in quasi-equilibrium. Disk self-gravity is insufficient to create the perturbation. This behavior may be related either to an early phase of star formation in which the Keplerian regime is not yet fully established and/or to a disturbance of yet unknown origin. An alternate, but unproven, possibility is that of a low mass companion located about 40 AU from AB Aur.
The acoustic, the digital and the body: a survey on musical instruments

This paper reports on a survey conducted in the autumn of 2006 with the objective to understand people's relationship to their musical tools. The survey focused on the question of embodiment and its different modalities in the fields of acoustic and digital instruments. The questions of control, instrumental entropy, limitations and creativity were addressed in relation to people's activities of playing, creating or modifying their instruments. The approach used in the survey was phenomenological, i.e. we were concerned with the experience of playing, composing for and designing digital or acoustic instruments. At the time of analysis, we had 209 replies from musicians, composers, engineers, designers, artists and others interested in this topic. The survey was mainly aimed at instrumentalists and people who create their own instruments or compositions in flexible audio programming environments such as SuperCollider, Pure Data, ChucK, Max/MSP, CSound, etc.
In-vivo implant mechanics of flexible, silicon-based ACREO microelectrode arrays in rat cerebral cortex

The mechanical behavior of an electrode during implantation into neural tissue can have a profound effect on the neural connections and signaling that takes place within the tissue. The objective of the present work was to investigate the in vivo implant mechanics of flexible, silicon-based ACREO microelectrode arrays recently developed by the VSAMUEL consortium (European Union, grant #IST-1999-10073). We have previously reported on both the electrical [1]-[3] and mechanical [4], [5] properties of the ACREO electrodes. In this paper, the tensile and compression forces were measured during a series of in vivo electrode insertions into the cerebral cortex of rats (7 acute experiments, 2-mm implant depth, 2-mm/s insertion velocity). We compared the ACREO silicon electrodes (4' opening angle, 1-8 shafts) to single-shaft tungsten electrodes (3' and 10' opening angles). The penetration force and dimpling increased with the cross-sectional area (statistical difference between the largest and the smallest electrode) and with the number of shafts (no statistical difference). We consistently observed tensile (drag) forces during the retraction phase, which indicates the brain tissue sticks to the electrode within a short time period. Treating the electrodes prior to insertion with silane (hydrophobic) or piranha (hydrophilic) significantly decreased the penetration force. In conclusion, our findings suggest that reusable electrodes for acute animal experiments must not only be strong enough to survive a maximal force that exceeded the penetration force, but must also be able to withstand high tension forces during retraction. Careful cleaning is not only important to avoid foreign body response, but can also reduce the stress applied to the electrode while penetrating the brain tissue
The development of mental toughness in adolescents: utilising established theories

This thesis explored and evaluated the appropriateness of established psychological theories for understanding mental toughness development in adolescents. Initially, adolescent performers’ perspectives about mental toughness development were grounding in Bronfenbrenner’s (2001) bioecological model. Subsequently, self-determination theory (SDT, Deci & Ryan, 1985b, 2000) was considered. This theory was selected because of its consistencies with the bioecological model and initial findings, as well as its potential to inform applied protocols. Significant theoretically-expected associations were identified between SDT principles and mental toughness, as well as mental toughness and other meaningful outcomes. The effectiveness of an intervention informed by SDT principles was then evaluated. Although findings did not support the hypotheses, several barriers and obstacles to adopting SDT principles in practice were identified. To elucidate the hypothesised associations, a conceptual essay that detailed the value of SDT for understanding mental toughness was presented. This essay conceptualised mental toughness as comprising notions of striving, surviving, and thriving. It is hoped that researchers will continue to investigate the development of mental toughness along the lines pursued in this thesis and, at the same time, attend to recommendations proposed throughout.
Analysis of k-Nearest Neighbor Distances with Application to Entropy Estimation

Estimating entropy and mutual information consistently is important for many machine learning applications. The Kozachenko-Leonenko (KL) estimator (Kozachenko & Leonenko, 1987) is a widely used nonparametric estimator for the entropy of multivariate continuous random variables, as well as the basis of the mutual information estimator of Kraskov et al. (2004), perhaps the most widely used estimator of mutual information in this setting. Despite the practical importance of these estimators, major theoretical questions regarding their finite-sample behavior remain open. This paper proves finite-sample bounds on the bias and variance of the KL estimator, showing that it achieves the minimax convergence rate for certain classes of smooth functions. In proving these bounds, we analyze finite-sample behavior of k-nearest neighbors (k-NN) distance statistics (on which the KL estimator is based). We derive concentration inequalities for k-NN distances and a general expectation bound for statistics of k-NN distances, which may be useful for other analyses of k-NN methods.
Noninvasive chemical enucleation of mouse oocytes

A noninvasive method of enucleating mouse oocytes has been developed and evaluated. Strong chromosome to chromosome binding was induced by culturing early metaphase I oocytes in etoposide supplemented medium. Subsequent expulsion of the entire chromosome complex during polar body extrusion was facilitated by exposing the etoposide treated oocytes to a combination of cycloheximide and etoposide during anaphase and telophase. This simple two‐step chemical enucleation procedure yields fully enucleated mouse oocytes in 96% of cases. Chemically enucleated oocytes do not contain maturation promoting factor (MPF) at the end of etoposide‐cycloheximide enucleation. MPF levels are, however, restored during subsequent incubation in drug‐free medium and, after 15 h of post‐enucleation culture, the cytoplasts regain their full capacity for parthenogenetic activation and nuclear remodelling. We believe that this novel enucleation technique will greatly facilitate the research in nuclear transplantation. © 1993 Wiley‐Liss, Inc.
In Vitro and In Vivo Effects of Adrenaline and Phentolamine on Platelet Function

Summary In vitro and in vivo effects of adrenaline (ADR) on platelet aggregation, on platelet factor 3 (PF3) availability and on platelet factor 4 (PF4) release were studied in man. Inhibitory action of an alpha-blocker, phentolamine (PHEN) was investigated in the same conditions. The threshold concentration (TC) of ADR inducing the typical two-phase response in aggregation tests when added to platelet-rich plasma (PRP) varied in different pools of plasma, but always induced an evident PF4 release and increased PF3 availability. A further increase in both parameters was obtained with higher concentrations but without any significant dose/response correlation. Adding PHEN alone to PRP did not induce platelet aggregation or modify PF4 release induced by stirring, but it reduced PF3 availability. On the other hand, PHEN prevented the effects of ADR in different platelet tests, at appropriate concentrations. Intravenous infusion of ADR lowered the TC, and increased PF3 availability and PF4 release. In vivo administration of PHEN, in contrast, increased TC and reduced PF3 availability, while PF4 remained unchanged.
Effects of caffeic acid phenethyl ester on glycerol‐induced acute renal failure in rats

1. Free radicals and nitric oxide (NO) play a crucial role in the pathogenesis of myoglobinuric acute renal failure (ARF). The aim of the present study was to investigate the effects of caffeic acid phenethyl ester (CAPE), an anti‐oxidant, on the myoglobinuric ARF induced by intramusculer hypertonic glycerol injection.