Miracle-dz/UniFAR-FTUs huggingface dataset:
EVOLUTION OF LATE‐LIFE MORTALITY IN DROSOPHILA MELANOGASTER

Abstract. — Aging appears to cease at late ages, when mortality rates roughly plateau in large‐scale demographic studies. This anomalous plateau in late‐life mortality has been explained theoretically in two ways: (1) as a strictly demographic result of heterogeneity in life‐long robustness between individuals within cohorts, and (2) as an evolutionary result of the plateau in the force of natural selection after the end of reproduction. Here we test the latter theory using cohorts of Drosophila melanogaster cultured with different ages of reproduction for many generations. We show in two independent comparisons that populations that evolve with early truncation of reproduction exhibit earlier onset of mortality‐rate plateaus, in conformity with evolutionary theory. In addition, we test two population genetic mechanisms that may be involved in the evolution of late‐life mortality: mutation accumulation and antagonistic pleiotropy. We test mutation accumulation by crossing genetically divergent, yet demographically identical, populations, testing for hybrid vigor between the hybrid and nonhybrid parental populations. We found no difference between the hybrid and nonhybrid populations in late‐life mortality rates, a result that does not support mutation accumulation as a genetic mechanism for late‐life mortality, assuming mutations act recessively. Finally, we test antagonistic pleiotropy by returning replicate populations to a much earlier age of last reproduction for a short evolutionary time, testing for a rapid indirect response of late‐life mortality rates. The positive results from this test support antagonistic pleiotropy as a genetic mechanism for the evolution of late‐life mortality. Together these experiments comprise the first corroborations of the evolutionary theory of late‐life mortality.
Clinical Outcomes of an Optimized Prolate Ablation Procedure for Correcting Residual Refractive Errors Following Laser Surgery

Purpose The purpose of this study was to investigate the clinical efficacy of an optimized prolate ablation procedure for correcting residual refractive errors following laser surgery. Methods We analyzed 24 eyes of 15 patients who underwent an optimized prolate ablation procedure for the correction of residual refractive errors following laser in situ keratomileusis, laser-assisted subepithelial keratectomy, or photorefractive keratectomy surgeries. Preoperative ophthalmic examinations were performed, and uncorrected distance visual acuity, corrected distance visual acuity, manifest refraction values (sphere, cylinder, and spherical equivalent), point spread function, modulation transfer function, corneal asphericity (Q value), ocular aberrations, and corneal haze measurements were obtained postoperatively at 1, 3, and 6 months. Results Uncorrected distance visual acuity improved and refractive errors decreased significantly at 1, 3, and 6 months postoperatively. Total coma aberration increased at 3 and 6 months postoperatively, while changes in all other aberrations were not statistically significant. Similarly, no significant changes in point spread function were detected, but modulation transfer function increased significantly at the postoperative time points measured. Conclusions The optimized prolate ablation procedure was effective in terms of improving visual acuity and objective visual performance for the correction of persistent refractive errors following laser surgery.
Germ-cell line and sexual differentiation in birds.

The present paper deals with recent investigations on the germ line and the sexual organogenesis in birds. The analysis has been limited to the following problems: origin of the germ line, physiology of the germinal epithelia, determinism of the migration of gonocytes, and differentiation of the germ cells during sexual organogenesis. It has been clearly established that in birds the germ line is precociously determined and that the anterior germinal crescent is a secondary formation. The hypothesis according to which the primary localization of the germ cells in birds (and more generally in Amniotes) would be posterior, is discussed. It appears to be the most plausible. The germinal epithelia are secretory and excretory organs. The excretory function is of the merocrine type. Kinetic studies of the protein turnover in the germinal epithelia demonstrate the existence of at least two categories of cytoplasmic proteins: structural proteins, and exportable proteins; the latter are excreted via protrusions of the epithelial cells. The hypothesis according to which the excretory function is associated with the attractive power exerted by the sexual primordia upon the migrating primordial germ cells is examined. The mechanism controlling the entry into the genital ridge of the gonocytes circulating in the embryonic blood stream is of a chemotactic nature. Finally, during early sexual organogenesis, as well as during later stages of sexual differentiation, the germ cells undergo important ultrastructural, histochemical and physiological (migratory properties) changes.
Development of the piezoelectric fiber and application for the smart board

In an attempt to develop piezoelectric sensor and actuator for smart board, complex piezoelectric fibers with metal core were fabricated by both hydrothermal method and extrusion method. The insertion of metal core was significant in view that the fragility of ceramics is overcome and electrodes are not required in the use as sensor and actuator. In order to evaluate the sensor and actuator abilities of these new-type fibers, a cantilever structure was constructed by embedding them into the surface of CFRP composite board. As a result of vibration of this CFRP board by electromagnetic vibrometer, it was found that the fiber has an obvious sensor function, since electric charge was output from the fiber in proportion to the vibration amplitude. On the contrary, it became also evident that the fiber functions as actuator, since the CFRP board was vibrated by applying an AC voltage between the metal core and CFRP matrix. It seemed likely that the hydrothermal fiber is adequate to sensor use, while the extruded fiber is suitable for actuator use because of the higher actuator power.
3D Menagerie: Modeling the 3D Shape and Pose of Animals

There has been significant work on learning realistic, articulated, 3D models of the human body. In contrast, there are few such models of animals, despite many applications. The main challenge is that animals are much less cooperative than humans. The best human body models are learned from thousands of 3D scans of people in specific poses, which is infeasible with live animals. Consequently, we learn our model from a small set of 3D scans of toy figurines in arbitrary poses. We employ a novel part-based shape model to compute an initial registration to the scans. We then normalize their pose, learn a statistical shape model, and refine the registrations and the model together. In this way, we accurately align animal scans from different quadruped families with very different shapes and poses. With the registration to a common template we learn a shape space representing animals including lions, cats, dogs, horses, cows and hippos. Animal shapes can be sampled from the model, posed, animated, and fit to data. We demonstrate generalization by fitting it to images of real animals including species not seen in training.
A Simple Rule for Dendritic Spine and Axonal Bouton Formation Can Account for Cortical Reorganization after Focal Retinal Lesions

Lasting alterations in sensory input trigger massive structural and functional adaptations in cortical networks. The principles governing these experience-dependent changes are, however, poorly understood. Here, we examine whether a simple rule based on the neurons' need for homeostasis in electrical activity may serve as driving force for cortical reorganization. According to this rule, a neuron creates new spines and boutons when its level of electrical activity is below a homeostatic set-point and decreases the number of spines and boutons when its activity exceeds this set-point. In addition, neurons need a minimum level of activity to form spines and boutons. Spine and bouton formation depends solely on the neuron's own activity level, and synapses are formed by merging spines and boutons independently of activity. Using a novel computational model, we show that this simple growth rule produces neuron and network changes as observed in the visual cortex after focal retinal lesions. In the model, as in the cortex, the turnover of dendritic spines was increased strongest in the center of the lesion projection zone, while axonal boutons displayed a marked overshoot followed by pruning. Moreover, the decrease in external input was compensated for by the formation of new horizontal connections, which caused a retinotopic remapping. Homeostatic regulation may provide a unifying framework for understanding cortical reorganization, including network repair in degenerative diseases or following focal stroke.
Biomimetic soft actuator: design, modeling, control, and applications

A new biomimetic linear actuator named Antagonistically Driven Linear Actuator (ANTLA) that could be directly employed in both macro and microscale of robotic applications is introduced in the present work. The presented actuator provides cost effectiveness and simple fabrication process thanks to its plain construction. In addition to producing basic bidirectional rectilinear motions, the actuator is able to modulate its compliance that might be one of the critical elements of the actuator functionality for the biomimetic applications. For the test, the proposed actuator concept is fabricated and assembled in a microscale robot that generates annelid motion.
Estrogen receptors (ERα/ERβ) in normal and pathological growth of the human myometrium: pregnancy and leiomyoma.

The distributions of the mRNAs for estrogen receptors (ERα and ERβ) and their binding properties in myometria of pregnant and nonpregnant women and in leiomyoma were studied. RT-PCR analysis indicated that the term pregnancy myometria had little ERα mRNA, whereas the amounts of ERβ mRNAs in pregnant or nonpregnant myometria appeared to be similar. Both ERα and ERβ mRNA were greater in certain leiomyoma than in normal nonpregnant myometria. The binding kinetics revealed that two specific binding sites (with high or low affinity) for 17β-estradiol were present in the nonpregnant myometrium. Only the low-affinity binding sites were detectable in late-pregnancy myometria and in leiomyoma, and their capacities were increased two- to threefold ( P < 0.001) in leiomyoma. The pregnancy- and leiomyoma-related changes in myometrial ER status, especially the low concentration of ERα mRNA and the lack of high-affinity ER in pregnant women, plus the increased ERα and ERβ mRNAs and the increased low-affinity ER in some leiomyoma, suggest that the redistribution of ER subtypes is associated with the pathological and/or normal growth of the myometrium.
Negative, zero and positive stiffness in extended Eshelby plates

Structures under loading can show positive and negative stiffness (during buckling) with zero stiffness just being one point of transition. Material structures with extended zero stiffness regimes have also been reported. Using the example of an extended Eshelby plate with a positive and negative edge dislocation, we show the existence of finite regimes of positive, zero and negative stiffness in a single system. Given that stable states/configurations of negative stiffness cannot exist in an isolated system; we show the existence of metastable states of negative stiffness along with unstable states of positive stiffness. The system also exhibits one point of unstable equilibrium.
De novo methylation of CpG island sequences in human fibroblasts overexpressing DNA (cytosine-5-)-methyltransferase

Recent studies showing a correlation between the levels of DNA (cytosine-5-)-methyltransferase (DNA MTase) enzyme activity and tumorigenicity have implicated this enzyme in the carcinogenic process. Moreover, hypermethylation of CpG island-containing promoters is associated with the inactivation of genes important to tumor initiation and progression. One proposed role for DNA MTase in tumorigenesis is therefore a direct role in the de novo methylation of these otherwise unmethylated CpG islands. In this study, we sought to determine whether increased levels of DNA MTase could directly affect CpG island methylation. A full-length cDNA for human DNA MTase driven by the cytomegalovirus promoter was constitutively expressed in human fibroblasts. Individual clones derived from cells transfected with DNA MTase (HMT) expressed 1- to 50-fold the level of DNA MTase protein and enzyme activity of the parental cell line or clones transfected with the control vector alone (Neo). To determine the effects of DNA MTase overexpression on CpG island methylation, we examined 12 endogenous CpG island loci in the HMT clones. HMT clones expressing > or = 9-fold the parental levels of DNA MTase activity were significantly hypermethylated relative to at least 11 Neo clones at five CpG island loci. In the HMT clones, methylation reached nearly 100% at susceptible CpG island loci with time in culture. In contrast, there was little change in the methylation status in the Neo clones over the same time frame. Taken together, the data indicate that overexpression of DNA MTase can drive the de novo methylation of susceptible CpG island loci, thus providing support for the idea that DNA MTase can contribute to tumor progression through CpG island methylation-mediated gene inactivation.
Statistical Transparency Analysis in Internet-Distributed Hardware-in-the-Loop Simulation

Internet-distributed hardware-in-the-loop simulation (ID-HILS) is emerging as a critical enabler for geographically dispersed concurrent systems engineering. This paper is concerned with transparency in ID-HILS, which is a measure of fidelity with respect to the nondistributed alternative of integration. Specifically, recognizing the need for a transparency analysis method for stochastic and nonlinear ID-HILS systems in general, the paper first proposes a statistical transparency analysis method. Next, this method is applied to a novel ID-HILS system. This application helps draw two important general conclusions: 1) Distributing the simulation can in and of itself be an important source of transparency degradation and can even dominate the adverse effects of the Internet's delay, jitter, and loss when delay is relatively small; and 2) transparency is not an independent property of the system, but is a system property that needs to be defined with respect to an output, as different output signals in the same system can experience different levels of transparency. These conclusions are important for guiding future efforts to improve transparency in a given ID-HILS system, and the proposed method enables such transparency analysis in other stochastic nonlinear ID-HILS systems, as well.
High-throughput purification of viral RNA based on novel aqueous chemistry for nucleic acid isolation.

BACKGROUND Extraction protocols using magnetic solid phases offer a high potential for automation. However, commercially available magnetic-bead-based assays either lack the sensitivity required for viral diagnostics or are disproportionately expensive. METHODS We developed an aqueous chemistry for extraction of viral nucleic acids from plasma samples by use of common magnetic silica beads. Nucleic acids were bound to the beads at acidic conditions in the presence of a kosmotropic salt and were eluted at a slightly alkaline pH. The method was implemented on a standard pipetting workstation for fully automated extraction of up to 48 samples of 240 muL plasma in 1 batch. RESULTS The detection limit of the method was comparable to the spin-column-based QIAamp Viral RNA Mini Kit, which relies on chaotropic salts and binding to a silica membrane, as the comparison method. The 95% detection limit was 23.1 IU per PCR for HIV-1 and 10.7 IU per PCR for hepatitis C virus (HCV). Suitability for clinical routine testing was confirmed in a total of 178 HIV-1- or HCV-positive plasma samples. The method linearity (R(2)) was >0.99 for the viruses evaluated. CONCLUSIONS Use of reagents without organic solvents allows simple and cost-effective automation of this method on common pipetting robots with low risk of contamination. Performance characteristics of the novel extraction method make it suitable for use in diagnosis of infectious diseases and viral load determinations.
Incremental Variability Management in Conceptual Data Models of Software Product Lines

Software Product Line Engineering is an approach to management of diversity in software families. Although several SPLE approaches exist in the domains of industrial software applications, product lines of data-intensive software systems have gained less attention. We use an incremental, delta-oriented technique to handle variability by specifying changes to be made to a core data model to define the data schemas of the products. We present a new merge-prune operator based on the superimposition of models as well as the structural well-formedness rules specified formally in Alloy. Our method provides a modular way to handle variability in data intensive systems. It is scalable with respect to the number of variation points in the system in contrast to the traditional annotative approaches for variability modeling. We have investigated the applicability of our approach by using it in a real-world case study.
Methods and strategies for gene structure curation in WormBase

The Caenorhabditis elegans genome sequence was published over a decade ago; this was the first published genome of a multi-cellular organism and now the WormBase project has had a decade of experience in curating this genome's sequence and gene structures. In one of its roles as a central repository for nematode biology, WormBase continues to refine the gene structure annotations using sequence similarity and other computational methods, as well as information from the literature- and community-submitted annotations. We describe the various methods of gene structure curation that have been tried by WormBase and the problems associated with each of them. We also describe the current strategy for gene structure curation, and introduce the WormBase ‘curation tool’, which integrates different data sources in order to identify new and correct gene structures. Database URL: http://www.wormbase. org/
External Ca effect on water permeability, regulatory volume decrease, and extracellular space in barnacle muscle cells.

The effect of extracellular Ca2+ (Cao) on sarcolemmal hydraulic water permeability (L'p), regulatory volume decrease (RVD), and extracellular space (ECS) was studied in barnacle muscle cells. Absence or presence of Cao had no effect on L'p [0 Cao = 2.762 +/- 0.098 x 10(-5), and 11 mM Cao = 2.720 +/- 0.222 x 10(-5) cm.kg. s-1 x osmol x 1-kgH2O-1]. Likewise, cells exposed to anisosmotic media (for < 30 min) behaved as osmometers in 0 and 11 mM Cao, showing similar slopes and intercepts in van't Hoff plots. At longer incubation times, however, hyposmotic conditions promoted a Cao-dependent RVD. The relationship between Cao and the percentage of cells responding with RVD to a hyposmotic challenge was sigmoidal (half-maximal Cao = 4.83 mM). The mean rate of RVD (40 nl/min) was independent of the level of swelling in response to hyposmotic challenges. However, the magnitude of RVD increased with larger hyposmotic challenges. Both the presence of Cao and hypotonicity reduced the "apparent" ECS by 47 +/- 6 and 39 +/- 6%, respectively. Three-dimensional reconstruction of autoradiographs of the cells was made to interpret these results.
Antioxidant activity of potato juice.

BACKGROUND The interest in potato juice as a therapeutic agent goes back to the 19th century but its application was not supported by any knowledge about biological activity of this raw material. Factors restricting the medical application of potato juice include its inattractive sensory and functional properties. The aim of the presented investigations was preliminary evaluation of the biological activity of potato juice and the impact on it of some technological operations such as: cryoconcentration and hydrolysis in a membrane reactor. MATERIAL AND METHODS Experiments comprised investigations of antioxidative potentials of fresh potato juice, products of its processing as well as fractions separated because of the size of their molecules using, for this purpose, Folin-Ciocalteu methods and reactions with the ABTS cation radical. RESULTS The value of the antioxidative potential of fresh potato juice determined by means of the ABTS reagent corresponded to approximately 330 μmol/100 g which is in keeping with literature data. As a result of the cryoconcentration process, the value determined by the Folin-Ciocalteu method was found to increase only slightly whereas the value determined by means of the ABTS reagent almost tripled. The antioxidative potential was found to grow even more strongly in the case of the application of both methods when the process of enzymatic hydrolysis was employed. The total of 5 protein fractions of molecular masses ranging from 11 000 Da to over 600 000 Da, as well as an organic non-protein fraction of the molecular mass of 600 Da, were obtained as a result of the performed separation. All the examined fractions exhibited antioxidative activities. The highest values determined by the Folin-Ciocalteu method were recorded for the protein fraction of 80 000 Da mean molecular mass, while using the ABTS reagent--for the organic, non-protein fraction. CONCLUSIONS Potato juice possesses antioxidative activity which can be enhanced by means of processing, especially, in the course of enzymatic hydrolysis. In addition, it was demonstrated that the organic nonprotein fraction of 600 Da mean molecular mass was characterised by the highest antioxidative activity.
On-Chip Power Distribution Grids With Multiple Supply Voltages for High-Performance Integrated Circuits

On-chip power distribution grids with multiple supply voltages are discussed in this paper. Two types of interdigitated and paired power distribution grids with multiple supply voltages and multiple grounds are presented. Analytic models are also developed to estimate the loop inductance in four types of proposed power delivery schemes. Two proposed schemes, fully and pseudo-interdigitated power delivery, reduce power supply voltage drops as compared to conventional interdigitated power distribution systems with dual supplies and a single ground by, on average, 15.3% and 0.3%, respectively. The performance of the proposed on-chip power distribution grids is compared to a reference power distribution grid with a single supply and a single ground. The voltage drop in fully interdigitated and fully paired power distribution grids with multiple supplies and multiple grounds is reduced, on average, by 2.7% and 2.3%, respectively, as compared to the voltage drop of an interdigitated power distribution grid with a single supply and a single ground. The proposed power distribution grids are a better alternative to a single supply voltage and a single ground power distribution system. On-chip resonances in power distribution grids with decoupling capacitors are intuitively explained in this paper, and circuit design implications are provided. It is also noted that fully interdigitated and fully paired power distribution grids with multiple supply voltages and multiple grounds are recommended to decouple power supply voltages.