gebhart/patrepeval huggingface dataset:
Migration depth and residence time of juvenile salmonids in the forebays of hydropower dams prior to passage through turbines or juvenile bypass systems: implications for turbine-passage survival (2015)

Little is known about the three-dimensional depth distributions in rivers of individually marked fish that are in close proximity to hydropower facilities. Knowledge of the depth distributions of fish approaching dams can be used to understand how vulnerable fish are to injuries such as barotrauma as they pass through dams. To predict the possibility of barotrauma injury caused by pressure changes during turbine passage, it is necessary to understand fish behaviour relative to acclimation depth in dam forebays as they approach turbines. A guiding study was conducted using high-resolution three-dimensional tracking results of salmonids implanted with Juvenile Salmon Acoustic Telemetry System transmitters to investigate the depth distributions of subyearling and yearling Chinook salmon (Oncorhynchus tshawytscha) and juvenile steelhead (Oncorhynchus mykiss) passing two dams on the Snake River in Washington State. Multiple approaches were evaluated to describe the depth at which fish were acclimated, and statistical analyses were performed on large data sets extracted from ∼28 000 individually tagged fish during 2012 and 2013. Our study identified patterns of depth distributions of juvenile salmonids in forebays prior to passage through turbines or juvenile bypass systems. This research indicates that the median depth at which juvenile salmonids approached turbines ranged from 2.8 to 12.2 m, with the depths varying by species/life history, year, location (which dam) and diel period (between day and night). One of the most enlightening findings was the difference in dam passage associated with the diel period. The amount of time that turbine-passed fish spent in the immediate forebay prior to entering the powerhouse was much lower during the night than during the day. This research will allow scientists to understand turbine-passage survival better and enable them to assess more accurately the effects of dam passage on juvenile salmon survival.
On Singular Moduli for Arbitrary Discriminants (2014)

Let &lt;f&gt;$d_1$&lt;/f&gt; and &lt;f&gt;$d_2$&lt;/f&gt; be discriminants of distinct quadratic imaginary orders &lt;f&gt;${{\\mathcal O}}_{d_1}$&lt;/f&gt; and &lt;f&gt;${{\\mathcal O}}_{d_2}$&lt;/f&gt; and let &lt;f&gt;$J(d_1,d_2)$&lt;/f&gt; denote the product of differences of CM &lt;f&gt;$j$&lt;/f&gt;-invariants with discriminants &lt;f&gt;$d_1$&lt;/f&gt; and &lt;f&gt;$d_2$&lt;/f&gt;. In 1985, Gross and Zagier gave an elegant formula for the factorization of the integer &lt;f&gt;$J(d_1,d_2)$&lt;/f&gt; in the case that &lt;f&gt;$d_1$&lt;/f&gt; and &lt;f&gt;$d_2$&lt;/f&gt; are relatively prime and discriminants of &lt;it&gt;maximal&lt;/it&gt; orders. To compute this formula, they first reduce the problem to counting the number of simultaneous embeddings of &lt;f&gt;${{\\mathcal O}}_{d_1}$&lt;/f&gt; and &lt;f&gt;${{\\mathcal O}}_{d_2}$&lt;/f&gt; into endomorphism rings of supersingular curves, and then solve this counting problem. Interestingly, this counting problem also appears when computing class polynomials for invariants of genus &lt;f&gt;$2$&lt;/f&gt; curves. However, in this application, one must consider orders &lt;f&gt;${{\\mathcal O}}_{d_1}$&lt;/f&gt; and &lt;f&gt;${{\\mathcal O}}_{d_2}$&lt;/f&gt; that are &lt;it&gt;non&lt;/it&gt;-maximal. Motivated by the application to genus &lt;f&gt;$2$&lt;/f&gt; curves, we generalize the methods of Gross and Zagier and give a computable formula for &lt;f&gt;$v_{\\ell }(J(d_1,d_2))$&lt;/f&gt; for any pair of discriminants &lt;f&gt;$d_1\\neq d_2$&lt;/f&gt; and any prime &lt;f&gt;$\\ell &gt; 2$&lt;/f&gt;. In the case that &lt;f&gt;$d_1$&lt;/f&gt; is squarefree and &lt;f&gt;$d_2$&lt;/f&gt; is the discriminant of any quadratic imaginary order, our formula can be stated in a simple closed form. We also give a conjectural closed formula when the conductors of &lt;f&gt;$d_1$&lt;/f&gt; and &lt;f&gt;$d_2$&lt;/f&gt; are relatively prime.
COSSMO: Predicting Competitive Alternative Splice Site Selection using Deep Learning (2018)

Abstract Motivation Alternative splice site selection is inherently competitive and the probability of a given splice site to be used also depends strongly on the strength of neighboring sites. Here we present a new model named Competitive Splice Site Model (COSSMO), which explicitly models these competitive effects and predict the PSI distribution over any number of putative splice sites. We model an alternative splicing event as the choice of a 3’ acceptor site conditional on a fixed upstream 5’ donor site, or the choice of a 5’ donor site conditional on a fixed 3’ acceptor site. We build four different architectures that use convolutional layers, communication layers, LSTMS, and residual networks, respectively, to learn relevant motifs from sequence alone. We also construct a new dataset from genome annotations and RNA-Seq read data that we use to train our model. Results COSSMO is able to predict the most frequently used splice site with an accuracy of 70% on unseen test data, and achieve an R 2 of 60% in modeling the PSI distribution. We visualize the motifs that COSSMO learns from sequence and show that COSSMO recognizes the consensus splice site sequences as well as many known splicing factors with high specificity. Availability Our dataset is available from http://cossmo.deepgenomics.com . Contact frey@deepgenomics.com Supplementary information Supplementary data are available at Bioinformatics online.
NTIRE 2022 Spectral Recovery Challenge and Data Set (2022)

This paper reviews the third biennial challenge on spectral reconstruction from RGB images, i.e., the recovery of whole-scene hyperspectral (HS) information from a 3-channel RGB image. This challenge presents the "ARAD_1K" data set: a new, larger-than-ever natural hyperspectral image data set containing 1,000 images. Challenge participants were required to recover hyper-spectral information from synthetically generated JPEG-compressed RGB images simulating capture by a known calibrated camera, operating under partially known parameters, in a setting which includes acquisition noise. The challenge was attended by 241 teams, with 60 teams com-peting in the final testing phase, 12 of which provided de-tailed descriptions of their methodology which are included in this report. The performance of these submissions is re-viewed and provided here as a gauge for the current state-of-the-art in spectral reconstruction from natural RGB images.
Power, Reliability, and Performance: One System to Rule them All (2016)

In a design based on the Charm++ parallel programming framework, an adaptive runtime system dynamically interacts with a datacenter's resource manager to control power by intelligently scheduling jobs, reallocating resources, and reconfiguring hardware. It simultaneously manages reliability by cooling the system to the running application's optimal level and maintains performance through load balancing.
Statistically Segregated k-Space Sampling for Accelerating Multiple-Acquisition MRI (2019)

A central limitation of multiple-acquisition magnetic resonance imaging (MRI) is the degradation in scan efficiency as the number of distinct datasets grows. Sparse recovery techniques can alleviate this limitation via randomly undersampled acquisitions. A frequent sampling strategy is to prescribe for each acquisition a different random pattern drawn from a common sampling density. However, naive random patterns often contain gaps or clusters across the acquisition dimension that, in turn, can degrade reconstruction quality or reduce scan efficiency. To address this problem, a statistically segregated sampling method is proposed for multiple-acquisition MRI. This method generates multiple patterns sequentially while adaptively modifying the sampling density to minimize k-space overlap across patterns. As a result, it improves incoherence across acquisitions while still maintaining similar sampling density across the radial dimension of k-space. Comprehensive simulations and in vivo results are presented for phase-cycled balanced steady-state free precession and multi-echo [Formula: see text]-weighted imaging. Segregated sampling achieves significantly improved quality in both Fourier and compressed-sensing reconstructions of multiple-acquisition datasets.
Direct measurement of quasiparticle evanescent waves in a dirty superconductor (2002)

We have used a perpendicular-current spin-polarization detector, in the form of a Permalloy-based exchange-biased spin valve, to measure the length scale for penetration of quasiparticles through superconducting-Nb thin films under diffusive transport conditions. In the low-temperature limit, this penetration length is $\ensuremath{\sim}16\mathrm{nm},$ comparable to the estimated ``dirty-limit'' zero-temperature coherence length of our Nb films.
Re: Radiotherapy to the Primary Tumour for Newly Diagnosed, Metastatic Prostate Cancer (STAMPEDE): a Randomised Controlled Phase 3 Trial (2019)

No AccessJournal of UrologyUrological Survey1 Jul 2019Re: Radiotherapy to the Primary Tumour for Newly Diagnosed, Metastatic Prostate Cancer (STAMPEDE): a Randomised Controlled Phase 3 Trial Samir S. TanejaMD Samir S. TanejaSamir S. Taneja More articles by this author View All Author Informationhttps://doi.org/10.1097/01.JU.0000557756.08329.16AboutFull TextPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "Re: Radiotherapy to the Primary Tumour for Newly Diagnosed, Metastatic Prostate Cancer (STAMPEDE): a Randomised Controlled Phase 3 Trial." The Journal of Urology, 202(1), pp. 32–33 Suggested Reading : Radical prostatectomy or external beam radiation therapy vs no local therapy for survival benefit in metastatic prostate cancer: a SEER-Medicare analysis. J Urol 2015; 194: 378. Link, Google Scholar © 2019 by American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetails Volume 202Issue 1July 2019Page: 32-33 Advertisement Copyright & Permissions© 2019 by American Urological Association Education and Research, Inc.MetricsAuthor Information Samir S. Taneja More articles by this author Expand All Advertisement Loading ...
Genetic aetiology of mood disorders (2012)

Abstract Advances towards the understanding of the etiological mechanisms involved in mood disorders provide interesting yet diverse hypotheses and promising models. In this context, molecular genetics has now been widely incorporated into genetic epidemiological research in psychiatry. Affective disorders and, in particular, bipolar affective disorder (BPAD) have been examined in many molecular genetic studies which have covered a large part of the genome, specific hypotheses such as mutations have also been studied. Most recent studies indicate that several chromosomal regions may be involved in the aetiology of BPAD. Other studies have reported the presence of anticipation in BPAD and in unipolar affective disorder (UPAD). In parallel to these new developments in molecular genetics, the classical genetic epidemiology, represented by twin, adoption and family studies, provided additional evidence in favour of the genetic hypothesis in mood disorders. Moreover, these methods have been improved through models to test the gene-environment interactions. In addition to genetic approaches, psychiatric research has focused on the role of psychosocial factors in the emergence of mood disorders. In this approach, psychosocial factors refer to the patient's social life context as well as to personality dimensions. Abnormalities in the social behavior such as impairment in social relationships have been observed during episode of affective disorders, and implicated in the etiology of affective disorders. Further, gender and socio-economic status also emerged as having a possible impact on the development of affective disorders. Finally, the onset and outcome of affective disorders could also be explained by interactions between the social life context and the individual's temperament and personality. The importance of temperament and personality characteristics in the etiology of depression has been emphasized in various theories, although disagreement exists with regard to terminology and the etiology. While significant advances have been done in these two major fields of research, it appears that integrative models, taking into account the interactions between biological (genetic) factors and social (psychosocial environment) variables offer the most reliable way to approach the complex mechanisms involved in the etiology and outcome of mood disorders. This chapter will review some of the most promising genetic and psychosocial hypotheses in mood disorders that can be integrated in interactive models.
Development of Spectral History and Pin Power Correction Methods for Pin-by-Pin Core Analysis Method Using Three-Dimensional Direct Response Matrix (2010)

Spectral history and pin power correction methods have been developed for the pin-by-pin core analysis method using the three-dimensional direct response matrix (3D-DRM). The direct response matrix is formalized using four subresponse matrices in order to respond to a core eigenvalue k and thus it can be recomposed at each outer iteration in the core analysis. For core analysis, it is necessary to take into account the historical effect, which is related to spectral heterogeneity. The spectral history method is used to evaluate the nodal burn-up spectrum obtained by using the outgoing neutron current instead of the nodal flux because the 3D-DRM method does not use the nodal flux. The pin power correction method corrects the fuel rod neutron production rates obtained in the pin-by-pin calculation. These two methods were tested in a heterogeneous system. The test results show that the neutron multiplication factor error and nodal neutron production rate errors can be reduced by half during burn-up. The root-mean-square differences between the relative fuel rod neutron production rate distributions and the maximum error of relative fuel rod production rate can also be reduced by half. This means that the developed methods can reflect the effects of intra- and interassembly heterogeneities during burn-up and can be used for core analysis.
MicroRNA signature of the human developing pancreas (2010)

We have determined specific groups of microRNAs in human fetal pancreas that change the degree of their expression throughout the development. A negative correlative analysis suggests an intertwined network of microRNAs and mRNAs collaborating with each other. This study provides information leading to potential two-way level of combinatorial control regulating gene expression through microRNAs targeting multiple mRNAs and, conversely, target mRNAs regulated in parallel by other microRNAs as well. This study may further the understanding of gene expression regulation in the human developing pancreas.
Quantification of angiotensin II-regulated proteins in urine of patients with polycystic and other chronic kidney diseases by selected reaction monitoring (2016)

We have optimized methods for quantification of Ang II-regulated proteins, and we demonstrated that they reflected differences in underlying kidney disease in this pilot study. High urine excretion of Ang II-regulated proteins in CKD patients likely reflects high kidney Ang II activity. Low excretion in ADPKD appears related to lack of communication between cysts and tubules. Future studies will determine whether urine excretion rate of Ang II-regulated proteins correlates with kidney Ang II activity in larger cohorts of chronic kidney disease patients.
Investigation of the <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:mmultiscripts><mml:mi>Pu</mml:mi><mml:mprescripts/><mml:none/><mml:mn>240</mml:mn></mml:mmultiscripts><mml:mo>(</mml:mo><mml:mi>n</mml:mi><mml:mo>,</mml:mo><mml:mi>f</mml:mi><mml:mo>)</mml:mo></mml:mrow></mml:math> reaction at the n_TOF/EAR2 facility in the 9 meV–6 MeV range (2020)

Background: Nuclear waste management is considered amongst the major challenges in the field of nuclear energy. A possible means of addressing this issue is waste transmutation in advanced nuclear systems, whose operation requires a fast neutron spectrum. In this regard, the accurate knowledge of neutron-induced reaction cross sections of several (minor) actinide isotopes is essential for design optimization and improvement of safety margins of such systems. One such case is $^{240}\mathrm{Pu}$, due to its accumulation in spent nuclear fuel of thermal reactors and its usage in fast reactor fuel. The measurement of the $^{240}\mathrm{Pu}(n,f)$ cross section was previously attempted at the CERN n_TOF facility EAR1 measuring station using the time-of-flight technique. Due to the low amount of available material and the given flux at EAR1, the measurement had to last several months to achieve a sufficient statistical accuracy. This long duration led to detector deterioration due to the prolonged exposure to the high $\ensuremath{\alpha}$ activity of the fission foils, therefore the measurement could not be successfully completed.Purpose: It is aimed to determine whether it is feasible to study neutron-induced fission at n_TOF/EAR2 and provide data on the $^{240}\mathrm{Pu}(n,f)$ reaction in energy regions requested for applications.Methods: The study of the $^{240}\mathrm{Pu}(n,f)$ reaction was made at a new experimental area (EAR2) with a shorter flight path which delivered on average 30 times higher flux at fast neutron energies. This enabled the measurement to be performed much faster, thus limiting the exposure of the detectors to the intrinsic activity of the fission foils. The experimental setup was based on microbulk Micromegas detectors and the time-of-flight data were analyzed with an optimized pulse-shape analysis algorithm. Special attention was dedicated to the estimation of the non-negligible counting loss corrections with the development of a new methodology, and other corrections were estimated via Monte Carlo simulations of the experimental setup.Results: This new measurement of the $^{240}\mathrm{Pu}(n,f)$ cross section yielded data from $9\phantom{\rule{4pt}{0ex}}\mathrm{meV}$ up to $6\phantom{\rule{4pt}{0ex}}\mathrm{MeV}$ incident neutron energy and fission resonance kernels were extracted up to $10\phantom{\rule{4pt}{0ex}}\mathrm{keV}$.Conclusions: Neutron-induced fission of high activity samples can be successfully studied at the n_TOF/EAR2 facility at CERN covering a wide range of neutron energies, from thermal to a few MeV.
Comparison of methods for management of measurement errors in surface topography measurements (2023)

Surface technology is essential to engineer surface properties by topologically optimised design or machining and finishing treatments. Optical surface topography measuring instruments represent state-of-the-art solution to characterise technological surfaces. Topographies measured by optical instruments are affected by errors (non-measured points and spikes), due to complex interactions between the measurand (the topography) and the instrument, liable of poor measurement quality and biasing characterisation. The literature proposes several approaches to manage measurement errors basing on empirical approaches (thresholding, interpolation) and machine learning modelling. This work compares the methods performances applied to industrially relevant case studies (highly polished and native additive manufacturing surfaces).
Software evolution storylines (2010)

This paper presents a technique for visualizing the interactions between developers in software project evolution. The goal is to produce a visualization that shows more detail than animated software histories, like code_swarm [15], but keeps the same focus on aesthetics and presentation. Our software evolution storylines technique draws inspiration from XKCD's "Movie Narrative Charts" and the aesthetic design of metro maps. We provide the algorithm, design choices, and examine the results of using the storylines technique. Our conclusion is that the it is able to show more details when compared to animated software project history videos. However, it does not scale to the largest projects, such as Eclipse and Mozilla.
Using Native Woody Plants for Phytomanagement of Urban Technosols Contaminated by Wood Pole Preservatives (2021)

Abstract Technosols are a major component of urban areas with little to no value, but many benefits can be gained by the use of native plants for their ecological reclamation. The aim of this study is to examine the capacity of North American native woody species to establish in and remediate a wood preservative‐contaminated technosol. Nine species are planted in mesocosms containing highly contaminated or non‐contaminated synthetic technosols. Remediation potential and plant physiology parameters (survival, photosynthesis and root growth) are monitored during one growing season. Results show an inverse relation between species performance ranking in the non‐contaminated technosol compared to ranking in contaminated soil. Overall, Salix bebbiana and Sambucus canadensis show good potential for phytomanagement of heterogenous contaminated technosols, offering the best compromise between performance in non‐contaminated and contaminated soils. Most species are able to phytoextract copper (Cu), with Rhus typhina , Alnus crispa , and S. bebbiana showing the highest Cu concentrations in stems. The use of multiple native species for technosol reclamation can be beneficial due to the heterogeneous nature of soil contaminants.
Strained Silicon–Germanium-on-Insulator n-Channel Transistor with Silicon Source and Drain Regions for Performance Enhancement (2007)

10.1143/JJAP.46.2062
Impairment of synaptic vesicle clustering and of synaptic transmission, and increased seizure propensity, in synapsin I-deficient mice. (1995)

Synapsin I has been proposed to be involved in the modulation of neurotransmitter release by controlling the availability of synaptic vesicles for exocytosis. To further understand the role of synapsin I in the function of adult nerve terminals, we studied synapsin I-deficient mice generated by homologous recombination. The organization of synaptic vesicles at presynaptic terminals of synapsin I-deficient mice was markedly altered: densely packed vesicles were only present in a narrow rim at active zones, whereas the majority of vesicles were dispersed throughout the terminal area. This was in contrast to the organized vesicle clusters present in terminals of wild-type animals. Release of glutamate from nerve endings, induced by K+,4-aminopyridine, or a Ca2+ ionophore, was markedly decreased in synapsin I mutant mice. The recovery of synaptic transmission after depletion of neurotransmitter by high-frequency stimulation was greatly delayed. Finally, synapsin I-deficient mice exhibited a strikingly increased response to electrical stimulation, as measured by electrographic and behavioral seizures. These results provide strong support for the hypothesis that synapsin I plays a key role in the regulation of nerve terminal function in mature synapses.