gebhart/patrepeval huggingface dataset:
Characterization of <i>FAE1</i> in the zero erucic acid germplasm of <i>Brassica rapa</i> L. (2015)

The modification of erucic acid content in seeds is one of the major goals for quality breeding in oil-yielding Brassica species. However, few low erucic acid (LEA) resources are available, and novel LEA genetic resources are being sought. Fatty acid elongase 1 (FAE1) is the key gene that controls erucic acid synthesis. However, the mechanism for erucic acid synthesis in B. rapa lacks systematic study. Here, we isolated zero erucic acid lines from 1981 Chinese landraces of B. rapa and found that the formation of LEA is not attributable to variations in FAE1 coding sequences, as reported for B. napus, but may be attributable to the decrease in FAE1 expression. Moreover, the FAE1 promoter sequences of LEA and high erucic acid materials shared 95% similarity. Twenty-eight bases deletions (containing a 24-base AT-rich region) were identified approximately 1300 bp upstream from the FAE1 start codon in the LEA accessions. The genotype with the deletions co-segregated with the LEA trait in the segregating population. This study isolated an LEA B. rapa resource that can be exploited in Brassica cultivation. The promoter variations might modify the expression level of FAE1, and the results shed light on novel regulation mechanisms for erucic acid synthesis.
Mechanism of Suppression of Chromosomal Instability by DNA Polymerase POLQ (2014)

Although a defect in the DNA polymerase POLQ leads to ionizing radiation sensitivity in mammalian cells, the relevant enzymatic pathway has not been identified. Here we define the specific mechanism by which POLQ restricts harmful DNA instability. Our experiments show that Polq-null murine cells are selectively hypersensitive to DNA strand breaking agents, and that damage resistance requires the DNA polymerase activity of POLQ. Using a DNA break end joining assay in cells, we monitored repair of DNA ends with long 3' single-stranded overhangs. End joining events retaining much of the overhang were dependent on POLQ, and independent of Ku70. To analyze the repair function in more detail, we examined immunoglobulin class switch joining between DNA segments in antibody genes. POLQ participates in end joining of a DNA break during immunoglobulin class-switching, producing insertions of base pairs at the joins with homology to IgH switch-region sequences. Biochemical experiments with purified human POLQ protein revealed the mechanism generating the insertions during DNA end joining, relying on the unique ability of POLQ to extend DNA from minimally paired primers. DNA breaks at the IgH locus can sometimes join with breaks in Myc, creating a chromosome translocation. We found a marked increase in Myc/IgH translocations in Polq-defective mice, showing that POLQ suppresses genomic instability and genome rearrangements originating at DNA double-strand breaks. This work clearly defines a role and mechanism for mammalian POLQ in an alternative end joining pathway that suppresses the formation of chromosomal translocations. Our findings depart from the prevailing view that alternative end joining processes are generically translocation-prone.
ChainerMN: Scalable Distributed Deep Learning Framework (2017)

One of the keys for deep learning to have made a breakthrough in various fields was to utilize high computing powers centering around GPUs. Enabling the use of further computing abilities by distributed processing is essential not only to make the deep learning bigger and faster but also to tackle unsolved challenges. We present the design, implementation, and evaluation of ChainerMN, the distributed deep learning framework we have developed. We demonstrate that ChainerMN can scale the learning process of the ResNet-50 model to the ImageNet dataset up to 128 GPUs with the parallel efficiency of 90%.
Deep Learning based Intraretinal Layer Segmentation using Cascaded Compressed U-Net (2021)

A bstract Intraretinal layer segmentation on macular optical coherence tomography (OCT) images generates non invasive biomarkers querying neuronal structures with near cellular resolution. While first deep learning methods have delivered promising results with high computing power demands, a reliable, power efficient and reproducible intraretinal layer segmentation is still an unmet need. We propose a cascaded two-stage network for intraretinal layer segmentation, with both networks being compressed versions of U-Net (CCU-INSEG). The first network is responsible for retinal tissue segmentation from OCT B-scans. The second network segments 8 intraretinal layers with high fidelity. By compressing U-Net, we achieve 392- and 26-time reductions in model size and parameters in the first and second network, respectively. Still, our method delivers almost similar accuracy compared to U-Net without additional constraints of computation and memory resources. At the post-processing stage, we introduce Laplacian-based outlier detection with layer surface hole filling by adaptive non-linear interpolation. We trained our method using 17,458 B-scans from patients with autoimmune optic neuropathies, i.e. multiple sclerosis, and healthy controls. Voxel-wise comparison against manual segmentation produces a mean absolute error of 2.3 μ m, which is 2.5x better than the device’s own segmentation. Voxel-wise comparison against external multicenter data leads to a mean absolute error of 2.6 μ m for glaucoma data using the same gold standard segmentation approach, and 3.7 μ m mean absolute error compared against an externally segmented reference data set. In 20 macular volume scans from patients with severe disease, 3.5% of B-scan segmentation results were rejected by an experienced grader, whereas this was the case in 41.4% of B-scans segmented with a graph-based reference method.
<title>Time-domain analysis simulation for advanced tracking</title> (1992)

TASAT is a complete end-to-end system simulation of tracking and pointing systems. It can currently model ground-based (GB), space-based (SB), and kinetic energy weapon (KEW) systems at a very high level of fidelity to assess system performance and design tradeoffs. It is primarily a time-domain analysis tool, but it can also perform frequency-domain analysis for performance and stability analysis. TASAT was built as a modular set of interacting routines that permit much more than end-to-end analysis. Specifically, subsystem and even component level analyses are available. The code treats all aspects of tracking and pointing systems using realistic, anchored imagery in a multiwavelength simulation. Some of the functions modeled include orbit propagation or launch trajectories, image rendering with high fidelity scattering calculations, atmospheric or optical blur point-spread functions (PSFs), image formation via convolution, realistic focal plane sensors including dead bands, sensor noise, and analog-to- digital conversion, and control system response. For GB applications, the atmospheric model is a novel treatment of the time average PSF after application of an adaptive optics system. Also, atmospheric tilt is modeled exactly. The code has applications beyond GB, SB, and KEW systems. It will treat imaging systems, tactical and strategic surveillance systems, and radar range gating. The paper provides an overview of the simulation architecture and presents results from analyses of each of the principal systems modeled in TASAT.
An Adaptive Framework for Classification of Concept Drift with Limited Supervision (2012)

This thesis deals with the problem of classification of data affected by concept drift. In particular, it investigates the area of unsupervised model updating in which a classification model is updated without using information about the changing distributions of the classes.\n An adaptive framework that contains an ensemble of classifiers is developed. These can be mature or naive. In particular, only mature classifiers generate decisions, through majority voting, while naive classifiers are candidate to become mature.\n The first novelty of the proposed framework is a technique of feedback that combines concepts from ensemble-learning with concepts from self-training. In particular, naive classifiers are trained using unlabelled data and labels generated by mature classifiers over that data, by means of voting. This technique allows updates of the model of the framework in absence of supervision, namely, without using the true classes of the data. The second novelty is a technique that infers the presence of concept drift by measuring the similarity between the decisions of mature classifiers and the decisions of naive classifiers. When concept drift is inferred, a naive classifier is selected to become mature, and a mature classifier is deleted.\n A series of experiments are performed. They show that the framework can classify data with Gaussian distribution, and that this capability regards different classification techniques. The experiments also reveal that the framework cannot deal with the concept drift of a uniformly distributed dataset. Moreover, further experiments show that the inference of drift combines quick adapation with low false detections, thus leading to higher classification performance than comparative methods. However, this technique is not able to detect concept drift if the classes are separable.
Combining model checking and testing with an application to reliability prediction and distribution (2013)

Testing provides a probabilistic assurance of system correctness. In general, testing relies on the assumptions that the system under test is deterministic so that test cases can be sampled. However, a challenge arises when a system under test behaves non-deterministiclly in a dynamic operating environment because it will be unknown how to sample test cases.
I want to answer; who has a question? (2011)

Yahoo! Answers is currently one of the most popular question answering systems. We claim however that its user experience could be significantly improved if it could route the "right question" to the "right user." Indeed, while some users would rush answering a question such as "what should I wear at the prom?," others would be upset simply being exposed to it. We argue here that Community Question Answering sites in general and Yahoo! Answers in particular, need a mechanism that would expose users to questions they can relate to and possibly answer.
Improving accuracy in robotized fibre placement using force and visual servoing external hybrid control scheme (2014)

Improvement of robotised fiber placement cell.
Biomarkers of Cell Senescence Assessed by Imaging Cytometry (2012)

The characteristic features of senescent cells such as their "flattened" appearance, enlarged nuclei and low saturation density at the plateau phase of cell growth, can be conveniently measured by image-assisted cytometry such as provided by a laser scanning cytometer (LSC). The "flattening" of senescent cells is reflected by a decline in local density of DNA-associated staining with 4,6-diamidino-2-phenylindole (DAPI) and is paralleled by an increase in nuclear area. Thus, the ratio of the maximal intensity of DAPI fluorescence per nucleus to the nuclear area provides a very sensitive morphometric biomarker of "depth" of senescence, which progressively declines during senescence induction. Also recorded is cellular DNA content revealing cell cycle phase, as well as the saturation cell density at plateau phase of growth, which is dramatically decreased in cultures of senescent cells. Concurrent immunocytochemical analysis of expression of p21(WAF1), p16(INK4a), or p27(KIP1) cyclin kinase inhibitors provides additional markers of senescence. These biomarker indices can be expressed in quantitative terms ("senescence indices") as a fraction of the same markers of the exponentially growing cells in control cultures.
[Polyvitaminization--an effective method of optimizing the vitamin status of children]. (1993)

Insufficient vitamin value of the food rations for children at nurseries is expressed in lowered levels of vitamins and their metabolites in the urine, as well as in a higher frequency of vitamin and, particularly, polyvitamin deficiency in children, especially, in the winter-spring period. Improvement of the quality and increasing the quantity of food, prophylactic administration of polyvitamins in the periods of higher vitamin deficiency would be effective and real ways for optimization of vitamin status of children. Dragee "Undevitum" and "Hexavitum" proved to be most effective among the prophylactic polyvitamins, the synergy of action of their components provides the improvement in the values of renal excretion of vitamins and their metabolites, as well as reduction in the frequency of micro-symptoms of polyvitamin deficiency.
한국 도시재생의 연성적 잠재역량 (2010)

This study aims to analyze the effect of potential resources on urban regeneration or regional growth in Korea. The potential resources belongs to soft power, which can be divided into four realms, namely, creative potential, planning potential, social potential, and cultural potential. According to...
A new type of force sensor for contact tasks (2002)

The present paper describes a new type of force sensor having the properties of passive compliance, capable of sensing two components of the contact force. The device is based on the use of simple single-component tactile sensors. It is especially convenient for placing on the gripper fingertips with the aim of controlling force along the object axis and obtaining information about the pressure profile at the contact surface between the object and the gripper. A sensor's prototype has been built and some of its basic features were experimentally verified.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Analysis of pore-fluid pressure gradient and effective vertical-stress gradient distribution in layered hydrodynamic systems (1998)

A theoretical analysis is carried out to investigate the pore-fluid pressure gradient and effective vertical-stress gradient distribution in fluid-saturated porous rock masses in layered hydrodynamic systems. Three important concepts, namely the critical porosity of a porous medium, the intrinsic pore-fluid pressure and the intrinsic effective vertical stress of the solid matrix, are presented and discussed. Using some basic scientific principles, we derive analytical solutions and explore the conditions under which either the intrinsic pore-fluid pressure gradient or the intrinsic effective vertical-stress gradient can be maintained at the value of the lithostatic pressure gradient. Even though the intrinsic pore-fluid pressure gradient can be maintained at the value of the lithostatic pressure gradient in a single layer, it is impossible to maintain it at this value in all layers in a layered hydrodynamic system, unless all layers have the same permeability and porosity simultaneously. However, the intrinsic effective vertical-stress gradient of the solid matrix can be maintained at a value close to the lithostatic pressure gradient in all layers in any layered hydrodynamic system within the scope of this study.
Instruction buffering exploration for low energy VLIWs with instruction clusters (2004)

For multimedia applications, loop buffering is an efficient mechanism to reduce the power in the instruction memory of embedded processors. In particular, software controlled clustered loop buffers are energy efficient. However current compilers for VLIW do not fully exploit the potentials offered by such a clustered organization This paper presents an algorithm to explore what is the optimal loop buffer configuration and the optimal way to use this configuration for an application or a set of applications. Results for the MediaBench application suite show an additional 18% reduction (on average) in energy in the instruction memory hierarchy as compared to traditional non-clustered approaches to the loop buffer without compromising performance.
Reviewing the trends of nursing doctoral thesis research in Hong Kong (2012)

This review aimed to analyze the trends and contributions of nursing doctoral theses produced in Hong Kong. A total of 56 nursing doctoral theses were included in this review. The most often studied topic was cardiovascular rehabilitation care (n = 9, 16%). More recently, the most often studied topics has been health technology advancements in nursing care (n = 6, 10.7%). The common trend of study methods was to be quantitative in nature. Of the total, 35 out of 56 were quantitative studies. Half were experimental/ quasi-experimental research studies (n = 28, 50%). For theoretical foundations or applications, the majority (n = 21, 36%) of doctoral theses had no specific theoretical/conceptual models as study frameworks. This trend indicates that there is space for improving the theoretical and philosophical foundation of nursing research in Hong Kong. For the contributions of doctoral thesis research, Hong Kong nursing scholars place more emphasis on direct enhancement of clinical practice or the improvement of patient outcomes. This review provides concrete evidence of the status of nursing research and knowledge development in Hong Kong nursing.
Controlled flooding in wireless ad-hoc networks (2006)

We show how flooding can be adopted as a reliable and efficient routing scheme in ad-hoc wireless mobile networks. It turns out that, with the assistance of some tunable heuristics, flooding is not necessarily inferior to sophisticated point-to-point forwarding schemes, at least for some classes of wireless applications. We discuss a reactive broadcast-based ad-hoc routing protocol in which flooding exhibits a tendency to converge to a narrow strip of nodes along the shortest path between source and destination. The width of this strip can be adjusted automatically or by the user, e.g., in response to varying node density and mobility patterns. Finally, we point out a certain deficiency inherent in the IEEE 802.11 family of collision avoidance schemes and show how to fix it to provide better service to broadcast-based routing schemes represented by our variant of controlled flooding.
An ultrasound indentation system for biomechanical properties assessment of soft tissues in-vivo (1996)

An ultrasound indentation system for biomechanical assessment of soft tissues in vivo was developed. The pen-size, hand-held probe was composed of an ultrasound transducer and a load cell. The ultrasound transducer was at the tip of the probe serving also as the indentor. The thickness and deformation of the soft tissue layer were determined from the ultrasound echo. A compressive load cell was connected in series with the ultrasound transducer to record the force response. A validation experiment was performed on porcine tissues. Force and deformation acquired with the present system was in good comparison with those obtained from a Housfield material testing machine. Material constants were obtained via a curve-fitting procedure by predicting the force transient response from the deformation-time data using a quasilinear viscoelastic model. In addition, deformation in the fat and in the muscle could be differentiated. The potential applications of this type of indentation probes are many. The specific application of this current development is for stump tissue assessment in the design of prosthetics.
Self-Limiting Layer Synthesis of Transition Metal Dichalcogenides (2016)

This work reports the self-limiting synthesis of an atomically thin, two dimensional transition metal dichalcogenides (2D TMDCs) in the form of MoS2. The layer controllability and large area uniformity essential for electronic and optical device applications is achieved through atomic layer deposition in what is named self-limiting layer synthesis (SLS); a process in which the number of layers is determined by temperature rather than process cycles due to the chemically inactive nature of 2D MoS2. Through spectroscopic and microscopic investigation it is demonstrated that SLS is capable of producing MoS2 with a wafer-scale (~10 cm) layer-number uniformity of more than 90%, which when used as the active layer in a top-gated field-effect transistor, produces an on/off ratio as high as 10(8). This process is also shown to be applicable to WSe2, with a PN diode fabricated from a MoS2/WSe2 heterostructure exhibiting gate-tunable rectifying characteristics.
Wheel and rail contact simulation using a twin disc tester (2009)

The contact between wheel and rail has been studied for many years in the field and using different test approaches. The wheel/rail contact in this work was simulated by a rolling-sliding twin disc contact machine. Currently this approach is widely accepted as a technique for studying different aspects of the wheel/rail contact such as; wear, rolling contact fatigue (RCF) crack propagation and issues concerning wheel/rail isolation.
Asymmetric information and electoral campaigns: the monitoring role of media (2004)

This paper analyzes an electoral game where candidates have private information on their own types. Candidates propose non-binding platforms and run for office. Voters make inferences on the politicians' types and cast their votes. We show that in this set-up, the existence of a media industry is desirable, as it improves the quality of the political game by increasing the accuracy of the candidates' signals. In particular, it induces politicians to discard the use of pooling strategies. We show that this monitoring role of the media is more likely to appear in societies with large numbers of swing voters, or with great competition among the media. We do this analysis in a context of a neutral media. We also analyze the case of an ideological media and show that ideology is not harmful per se, but the possibility of asymmetries in the support of different candidates may well be.
Chlorocarbon Activation: Catalytic Carbonylation of Dichloromethane and Chlorobenzene (1989)

Catalytic reactions of the type dichloromethane → ketene and chlorobenzene → benzoic acid esters (or benzaldehyde) are possible with Pd complexes, although the turnover numbers are still small. The CCl bond in CH2C12 is even activated by [Pd(PCy3)2(dba)]/PCy3 and the CCl bond in PhCI by Pd(CH3COO)2/PCy3 (Cy = cyclohexyl). The nature of the phosphane is decisive in these reactions : their basicity and cone angle must lie within a certain range. Initial products in the carbonylation are complexes 1 and 2.