gebhart/patrepeval huggingface dataset:
Horizontal transmission and recombination maintain forever young bacterial symbiont genomes (2019)

Abstract Bacterial symbionts bring a wealth of functions to the associations they participate in, but by doing so, they endanger the genes and genomes underlying these abilities. When bacterial symbionts become obligately associated with their hosts, their genomes are thought to decay towards an organelle-like fate due to decreased homologous recombination and inefficient selection. However, numerous associations exist that counter these expectations, especially in marine environments, possibly due to ongoing horizontal gene flow. Despite extensive theoretical treatment, no empirical study thus far has connected these underlying population genetic processes with long-term evolutionary outcomes. By sampling marine chemosynthetic bacterial-bivalve endosymbioses that range from primarily vertical to strictly horizontal transmission, we tested this canonical theory. We found that transmission mode strongly predicts homologous recombination rates, and that exceedingly low recombination rates are associated with moderate genome degradation in the marine symbionts with nearly strict vertical transmission. Nonetheless, even the most degraded marine endosymbiont genomes are occasionally horizontally transmitted and are much larger than their terrestrial insect symbiont counterparts. Therefore, horizontal transmission and recombination enable efficient natural selection to maintain intermediate symbiont genome sizes and substantial functional genetic variation. Author summary Symbiotic associations between bacteria and eukaryotes are ubiquitous in nature and have contributed to the evolution of radically novel phenotypes and niches for the involved partners. New metabolic or physiological capacities that arise in these associations are typically encoded by the bacterial symbiont genomes. However, the association itself endangers the retention of bacterial genomic coding capacity. Endosymbiont genome evolution theory predicts that when bacterial symbionts become restricted to host tissues, their populations cannot remove deleterious mutations efficiently. This ultimately results in their genomes degrading to small, function-poor states, reminiscent of organellar genomes. However, many ancient marine endosymbionts do not fit this prediction, but instead retain relatively large, gene-rich genomes, indicating that the evolutionary dynamics of this process need more thorough characterization. Here we show that on-going symbiont gene flow via horizontal transmission between bivalve hosts and recombination among divergent gammaproteobacterial symbiont lineages are sufficient to maintain large and dynamic bacterial symbiont genomes. These findings indicate that many obligately associated symbiont genomes may not be as isolated from one another as previously assumed and are not on a one way path to degradation.
On biologically conformal boost dose optimization (2003)

A method is described that allows the inclusion of biological imaging data in the optimization of intensity-modulated radiotherapy to produce dose boosts that conform with target subvolumes of potentially reduced radiosensitivity. The biological image (e.g. PET, fMRI, etc) is transformed into a dose efficiency distribution using a piecewise linear calibration function with a prescribed maximum boost factor. Instead of dose alone, the cost function of the optimization algorithm depends on the product of the physical dose times dose efficiency. An example case of a base-of-tongue tumour which was imaged with the hypoxia tracer fluoro-misonidazole is presented, showing the excellent capability of IMRT to produce dose distributions that conform to spatially variable dose prescriptions.
Female Reproductive Factors and Eye Disease in a Rural South Indian Population: The Aravind Comprehensive Eye Survey (2004)

Female reproductive factors do not appear to influence age-related cataract, open-angle glaucoma, macular degeneration or myopia significantly in rural south India.
Accuracy improvement in the TDR-based localization of water leaks (2016)

A time domain reflectometry (TDR)-based system for the localization of water leaks has been recently developed by the authors. This system, which employs wire-like sensing elements to be installed along the underground pipes, has proven immune to the limitations that affect the traditional, acoustic leak-detection systems. Starting from the positive results obtained thus far, in this work, an improvement of this TDR-based system is proposed. More specifically, the possibility of employing a low-cost, water-absorbing sponge to be placed around the sensing element for enhancing the accuracy in the localization of the leak is addressed. To this purpose, laboratory experiments were carried out mimicking a water leakage condition, and two sensing elements (one embedded in a sponge and one without sponge) were comparatively used to identify the position of the leak through TDR measurements. Results showed that, thanks to the water retention capability of the sponge (which maintains the leaked water more localized), the sensing element embedded in the sponge leads to a higher accuracy in the evaluation of the position of the leak.
Generation of binary vectors that optimize a given weight function with application to soft-decision decoding (2002)

Many decoding algorithms need to compute some lists of binary vectors that minimize a given weight function. Furthermore, it is often desirable that these vectors are generated by increasing weight. The considered weight function is usually decreasing in the a priori likelihood that the vector yields correct decoding. We present a new technique to generate candidates for error patterns from the most a priori likely to the least, that proves significantly more efficient than any other known method.
The effect of luminance texture on MAEs (2010)

Previous research on motion perception has found that static luminance texture produces an increase in the perceived speed of moving stimuli. The experiments discussed here study the influence of texture on another aspect of motion perception: the motion aftereffect (MAE). In Experiment 1, we measured static MAE duration in three conditions: 1- luminance modulated gratings to which no texture was added 2- luminance modulated gratings to which static texture (static luminance noise) was added 3- contrast modulated noise. Our results demonstrate that adding static luminance texture to a drifting luminance-modulated sinewave grating greatly diminishes static MAE duration and can even completely eliminate the static MAE. Our results also show that no difference in static MAE duration occurred between luminance-modulated gratings to which static luminance texture was added and contrast-modulated noise. This suggests that the failure of contrast-modulated texture to elicit a static MAE may not come from a fundamental difference in the processing of first- and second-order motion, but from the luminance texture inherently present in these second-order stimuli. Our results and the static MAE are discussed in a Bayesian context in which adaptation creates a shift in the prior's center in the direction opposite to the direction of adaptation and texture is used as a landmark. This is consistent with a recalibration and error-correcting account of the MAE. In Experiment 2, we studied the effects of texture characteristics on the MAE by notch-filtering the luminance noise in Fourier space. Preliminary data show that filtering out high pass information along the axis of motion produces longer MAE durations, but that filtering out high-pass information along an axis orthogonal to the axis of motion does not. This is consistent with the proposal that the visual system uses luminance texture in the assessment of motion.
Extension of Incomplete 3D for Arbitrary Multi-View-Synthesis. (2000)

The proposed approach is motivated by applications which allow user navigation and individual viewpoint specification in shared virtual environments with telepresence quality. In this context, we present a synthesis method for arbitrary virtual views in a multi-view camera set-up. This method generates a close to realtime, view adaptable reconstruction of a 3dimensional, (3D), object taken from at least two cameras. In this method, we use the recently developed Incomplete 3D, (IC3D), technique, a disparity-based multiview representation for a weakly convergent camera setup in combination with the trilinear warping functions to describe new virtual camera positions. Previously, only virtual views inside the baseline could be described by IC3D. Hence, user movement in virtual environments (VE) was restricted. In order to create a virtual camera position and orientation outside the baseline we apply point correspondences across the two reference images to a trilinear tensor, built from the fundamental matrix between the reference views. The trilinearities provide a general warping function from the reference images to virtual view that is governed directly by the virtual camera parameters.
Genetic Parameter Estimates for Postweaning Traits of Beef Cattle in a Stressful Environment (1989)

Data collected from 1957 through 1985 from a Hereford herd located in the Southwest were analyzed separately for each sex to evaluate the heritabilities of and genetic correlations among preweaning growth traits within groups of environmentally similar years. Data were grouped into years with poor, moderate and good environments based on contemporary group means for male calves' weaning weight. A total of 7,690 records were analyzed for birth weight, weaning weight and preweaning daily gain with a model that included year of birth, sire within year of birth, age of dam and a covariate of day of birth for birth weight or age at weaning for the weaning traits. Year of birth was a significant source of variation in all environments for all traits, accounting for more of the variation in the good and poor years than in moderate years. Heritability estimates for all traits were greater in good and moderate years than in poor years for bull calves. For heifers, however, estimates for weaning weight and preweaning daily gain were greater in the poor environment. Genetic correlations among birth weight and preweaning gain increased from the good environment to the poor environment (-.49 +/- .26 to .82 +/- .56 for male calves and -.09 +/- 2.6 to .46 +/- .25 for female calves) but phenotypic correlations were near zero in all environments.(ABSTRACT TRUNCATED AT 250 WORDS)
Outcome of Modified Kidner Procedure with Subtalar Arthroereisis for Painful Accessory Navicular Associated with Planovalgus Deformity (2012)

The modified Kidner procedure combined with a subtalar arthroereisis resulted in significant pain and functional improvement. The deformity correction obtained at surgery was maintained even if the arthroereisis plug was removed. The extra-articular plug did not lead to subtalar arthritis.
Slot-waveguide biochemical sensor (2007)

We report an experimental demonstration of an integrated biochemical sensor based on a slot-waveguide microring resonator. The microresonator is fabricated on a Si3N4-SiO2 platform and operates at a wavelength of 1.3 microm. The transmission spectrum of the sensor is measured with different ambient refractive indices ranging from n=1.33 to 1.42. A linear shift of the resonant wavelength with increasing ambient refractive index of 212 nm/refractive index units (RIU) is observed. The sensor detects a minimal refractive index variation of 2x10(-4) RIU.
Rapport I.5. : Contribution expérimentale à l’étude de l’influence du drainage sur les écoulements en rivière (1986)

Plus Bertrand, Lalanne-Berdouticq Gérard. Rapport I.5. : Contribution expérimentale à l’étude de l’influence du drainage sur les écoulements en rivière. In: L'impact des activités humaines sur les eaux continentales. Dix neuvièmes journées de l'hydraulique, Paris 9-11 septembre 1986. Tome 1, 1986.
Vventure capitalists (1981)

IN 1980, venture capitalists invested almost $1 billion in the growth businesses and emerging industries of the future. Eighty percent of this investment was made by the 100 or so leading venture capital firms. These professionally managed venture capital firms are dedicated to identifying business opportunities that can become major corporations within ten years. These venture‐capital‐financed companies will play key roles in defining the future competitive environment of present corporations, so tracking these firms is one way of keeping an eye on the future.
A pixelated MIMO wireless optical communication system (2006)

This paper introduces the pixelated wireless optical channel, which transmits data at high rates using a series of coded time-varying images. This multiple-input/multiple-output point-to-point wireless optical channel uses arrays of optical intensity transmitters and detectors to exploit the inherent spatial degrees of freedom and to realize significant gains in spectral efficiency over single-element systems. Spatial discrete multitone modulation is introduced as a means to combat low-pass spatial distortion and to alleviate spatial alignment problems of previous systems. The capacity of pixelated wireless optical channels is estimated by way of a water-pouring spectrum. A proof-of-concept experimental prototype is constructed using a 512times512 pixel liquid crystal display panel and 154times154 pixels of a charge-coupled device camera. A channel model is developed and the capacity estimated to be 22.4 kb/frame. An unoptimized multilevel code and multistage decoder is applied over the spatial frequency bins and shown to yield spectral efficiencies of approximately 1.7 kb/s/Hz over a range of 2 m
A compound heterozygote patient with Ehlers-Danlos syndrome type VI has a deletion in one allele and a splicing defect in the other allele of the lysyl hydroxylase gene (1998)

We report the first deletion mutation and the first splicing defect in the lysyl hydroxylase gene in a compound heterozygote patient with Ehlers-Danlos syndrome type VI with markedly reduced lysyl hydroxylase activity. Northern analysis of the RNA isolated from skin fibroblasts of the patient demonstrated the presence of a truncated lysyl hydroxylase mRNA. PCR and sequence analysis confirmed the truncation and indicated that the cells contain two types of shortened mRNAs, one lacking the sequences corresponding to exon 16 and the other lacking that corresponding to exon 17 of the lysyl hydroxylase gene. Analysis of genomic DNA revealed deletion of the penultimate adenosine from the 3' end of intron 15 from one allele. This defect was probably responsible for the skipping of exon 16 sequences from the transcript. The other allele, inherited from the mother, contains an Alu-Alu recombination with a deletion of about 3,000 nucleotides from the gene; this abnormality explains the lack of exon 17 sequences. The identified mutations in exon 16 and exon 17 do not alter the reading frame of the transcripts.
The adaptation of waste-to-energy technologies: towards the conversion of municipal solid waste into a renewable energy resource (2019)

Currently, there are an estimated 1.3 billion tonnes of municipal solid waste (MSW) generated per year globally, and this quantity is predicted to increase to 2.2 billion tonnes annually by 2025. If not well treated, this rapid growth of waste products can lead to socio-economic and environmental problems. Waste is potentially a misplaced valuable resource that can be converted and utilized in different ways such as renewable energy resources for the realization of sustainable development. Presently, waste-to-energy technologies (WtETs) are considered to be an encouraging advanced technology that is applied to convert MSW into a renewable energy resource (methane, biogas, biofuels or biodiesel, ethanol, syngas, or alcohol). WtETs can be biochemical (fermentation, anaerobic digestion, landfill with gas capture, and microbial fuel cell), thermochemical (incineration, thermal gasification, and pyrolysis), or chemical (esterification). This review mainly aims to provide an overview of the applications of these technologies by focusing on anaerobic digestion as biological (nonthermal) treatment technologies, and incineration, pyrolysis, and gasification processes as thermal treatment processes. Landfill gas utilization technologies, biological hydrogen production processes, and microbial fuel cells also are assessed. In addition, the contemporary risks and challenges of WtETs are reviewed.
A Media Access Protocol for Proactive Presence Discovery in Ubiquitous Wireless Networks (2008)

This paper proposes a MAC protocol for presence information discovery in ubiquitous networks. The proposed protocol is designed for proactive discovery in which wireless devices periodically broadcast packets containing presence information. The protocol is based on Framed Aloha. The objective of the protocol is to assure the discovery time of single-hop neighbors considering wireless collisions and also power consumption. In this paper, we show that the proposed protocol is able to assure specified discovery time in distributed networks with random topology.
Adaptive-neighborhood speckle removal in multitemporal synthetic aperture radar images (2001)

We present a new method for multitemporal synthetic aperture radar image filtering using three-dimensional (3D) adaptive neighborhoods. The method takes both spatial and temporal information into account to derive the speckle-free value of a pixel. For each pixel individually, a 3D adaptive neighborhood is determined that contains only pixels belonging to the same distribution as the current pixel. Then statistics computed inside the established neighborhood are used to derive the filter output. It is shown that the method provides good results by drastically reducing speckle over homogeneous areas while retaining edges and thin structures. The performances of the proposed method are compared in terms of subjective and objective measures with those given by several classical speckle-filtering methods.
The determinants of cleaner energy innovations of the world’s largest firms: the impact of firm learning and knowledge capital (2016)

In this paper, we address the determinants of clean energy inventions by 946 large firms. We use a new set of large firms’ patent portfolios and we broaden and deepen existing literature on this issue in two main ways: first, we conduct our study directly at the firm level and not at the industry or national levels and second, we do not focus on a single industry but encompass all industrial sectors. Drawing on firm (internal and external) knowledge and knowledge accumulation, we show there is a robust positive association between the (past) knowledge accumulated capital related to clean technologies and the number of inventions produced in that field, even after controlling for industry and nation fixed effects and other factors. The same relation works for (past) knowledge-accumulated capital in other (non-clean) technologies. However, the relation’s impact on the number of clean inventions produced is much lower. The magnitudes of our coefficient are in line with that obtained previously on firms in the auto-industry or at the sectoral level.
Distinct conformational states of SARS-CoV-2 spike protein (2020)

The ongoing SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) pandemic has created urgent needs for intervention strategies to control the crisis. The spike (S) protein of the virus forms a trimer and catalyzes fusion between viral and target cell membranes - the first key step of viral infection. Here we report two cryo-EM structures, both derived from a single preparation of the full-length S protein, representing the prefusion (3.1Å resolution) and postfusion (3.3Å resolution) conformations, respectively. The spontaneous structural transition to the postfusion state under mild conditions is independent of target cells. The prefusion trimer forms a tightly packed structure with three receptor-binding domains clamped down by a segment adjacent to the fusion peptide, significantly different from recently published structures of a stabilized S ectodomain trimer. The postfusion conformation is a rigid tower-like trimer, but decorated by N-linked glycans along its long axis with almost even spacing, suggesting possible involvement in a mechanism protecting the virus from host immune responses and harsh external conditions. These findings advance our understanding of how SARS-CoV-2 enters a host cell and may guide development of vaccines and therapeutics.
Fabrication, Characterization and Simulation of Sputtered Pt/In-Ga-Zn-O Schottky Diodes for Low-Frequency Half-Wave Rectifier Circuits (2020)

Amorphous In-Ga-Zn-O (IGZO) is a high-mobility semiconductor employed in modern thin-film transistors for displays and it is considered as a promising material for Schottky diode-based rectifiers. Properties of the electronic components based on IGZO strongly depend on the manufacturing parameters such as the oxygen partial pressure during IGZO sputtering and post-deposition thermal annealing. In this study, we investigate the combined effect of sputtering conditions of amorphous IGZO (In:Ga:Zn=1:1:1) and post-deposition thermal annealing on the properties of vertical thin-film Pt-IGZO-Cu Schottky diodes, and evaluated the applicability of the fabricated Schottky diodes for low-frequency half-wave rectifier circuits. The change of the oxygen content in the gas mixture from 1.64% to 6.25%, and post-deposition annealing is shown to increase the current rectification ratio from 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">5</sup> to 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">7</sup> at ±1 V, Schottky barrier height from 0.64 eV to 0.75 eV, and the ideality factor from 1.11 to 1.39. Half-wave rectifier circuits based on the fabricated Schottky diodes were simulated using parameters extracted from measured current-voltage and capacitance-voltage characteristics. The half-wave rectifier circuits were realized at 100 kHz and 300 kHz on as-fabricated Schottky diodes with active area of 200 μm × 200 μm, which is relevant for the near-field communication (125 kHz - 134 kHz), and provided the output voltage amplitude of 0.87 V for 2 V supply voltage. The simulation results matched with the measurement data, verifying the model accuracy for circuit level simulation.