gebhart/patrepeval huggingface dataset:
Amino acid analysis at the picomole level. Application to the C-terminal sequence analysis of polypeptides (1981)

Amino acids labelled with dimethylaminoazobenzenesulphonyl chloride can be separated by reversed-phase high-pressure liquid chromatography and detected in the visible region (436 nm). All 19 naturally occurring amino acids can be separated on a Zorbax ODS column by employing two different gradient systems consisting of an acetonitrile/aqueous buffer mixture. As little as 2--5 pmol of an individual dimethylaminoazobenzenesulphonyl-amino acid can be quantitatively analysed with reliability, and only 10--30 ng of the dimethylaminoazobenzenesulphonylated protein hydrolysate is needed for each complete amino acid analysis. This new technique is as sensitive as any of the current amino acid analysis methods involving ion-exchange separation plus fluorescence detection, and is technically much simpler. By the combination of this sensitive amino acid-analysing technique with carboxypeptidase, we have been able to determine the C-terminal sequence of polypeptides at the picomole level.
An intrinsic reward for affordance exploration (2009)

In this paper, we present preliminary results demonstrating how a robot can learn environmental affordances in terms of the features that predict successful control and interaction. We extend previous work in which we proposed a learning framework that allows a robot to develop a series of hierarchical, closed-loop manipulation behaviors. Here, we examine a complementary process where the robot builds probabilistic models about the conditions under which these behaviors are likely to succeed. To accomplish this, we present an intrinsic reward function that directs the robot's exploratory behavior towards gaining confidence in these models. We demonstrate how this single intrinsic motivator can lead to artifacts of behavior such as ldquonovelty,rdquo ldquohabituation,rdquo and ldquosurprise.rdquo We present results using the bimanual robot Dexter, and explore these results further in simulation.
Massively multiplex single-molecule oligonucleosome footprinting (2020)

These are the intermediate data used in "Massively multiplex single-molecule oligonucleosome footprinting", where the nonspecific adenine methyltransferase EcoGII was used to footprint accessible chromatin, and the methylation was then read using the Pacific Biosciences sequencing platform. The files here are intermediate outputs that capture metrics about the inter-pulse distance values as well as predictions of methylation status. The .npy, .feather, and .pickle files are the output of extractIPD.py, and callNucPeaks.py. The .csv is the output of a cell in SAMOSA_analyses.ipynb. All of this code can be found at https://github.com/RamaniLab/SAMOSA, including SAMOSA_analyses.ipynb which contains all downstream analyses that were performed on this data. <strong>meanIPDinfoChrControls.csv</strong>: This contains the data used to generate Supplementary Figures 2 and 3. It contains various summary measurements of the IPD values in each molecule of the <em>in vitro</em> samples <strong>Files ending in _bingmm.npy:</strong> These contain the posterior probability of adenines being methylated for the <em>in vitro</em> data. The files beginning with pbrun3 were sequenced on the Sequel I, and the files beginning with pbrun4 or pbrun5 were sequenced on the Sequel II. Other than Supplementary Figures 2 and 3, the analysis in the paper was based on the Sequel II data. naked_neg and DNA_minusM are both negative controls. naked_methyl and DNA_plusM are positive controls. chromatin samples are <em>in vitro</em> assembled chromatin. <strong>pbrun4_gold_nuc47_chromatin_peaks.feather</strong>: The estimated nucleosome centers from the <em>in vitro</em> assembled chromatin, in a data frame. Each row is an individual nucleosome dyad prediction. <strong>Files ending in _onlyT_zmwinfo.pickle</strong>: These files each contain a pandas data frame containing information about each molecule sequenced in the <em>in vivo</em> samples. These should be read in in python using the pandas read_pickle function, and require the same namespace as was used when saving them, so pandas must be imported as pd, and numpy as np. The neg samples are deproteinated unmethylated molecules, the pos samples are deproteinated methylated molecules, and the chromatin samples are methylated chromatin. <strong>Files ending in _bingmm.pickle</strong>: These files contain the posterior probability of being methylated for each adenine in each DNA molecule in the sample. They each have a corresponding zmwinfo file described above, and similarly must be read in with numpy imported as np. Each file is a dictionary with the zero-mode waveguide (ZMW) hole number as a key, and the value a numpy array with length equal to the unaligned CCS of that molecule, with methylation posterior probabilities at each A/T base. The zmwinfo dataframe has a 'zmw' column that can be used to match the information in that file with the methylation information in this one.
Capillary optics for radiation focusing (1996)

Capillary lens technology may ultimately bring benefits to neutron and x-ray-based science like conventional lenses with visible light. Although the technology is not yet 10 years old, these lenses have already had a significant impact in engineering, science, and medicine. Capillary lenses are advantageous when it is desirable to increase the radiation flux at a location without regard to its angular divergence. PNNL has worked to improve the technology in several ways. A single, optimally tapered capillary was manufactured, which allows intensity gains of a factor of 270 for an initially parallel, incident x-ray beam. Feasibility of constructing neutron lenses using {sup 58}Ni (particularly effective at reflecting neutrons) has been explored. Three applications for capillary optics have been identified and studied: neutron telescope, Gandolphi x-ray diffractometry, and neutron radiotherapy. A brief guide is given for determining which potential applications are likely to be helped by capillary optics.
Development of a Chirality-Sensitive Flexibility Descriptor for 3+3D-QSAR (2006)

Multidimensional QSAR methodologies can be used to predict the active conformation encoded in the conformational preferences of molecules in an active series by utilizing conformational sampling. In the 3+3D-QSAR approach, the conformational free energy loss is modeled with internal coordinate-based flexibility descriptors. While the pharmacophore point pair distance descriptors introduced earlier proved useful in the construction of QSAR models and in the prediction of important features of the active conformation, they are inherently incapable of describing the chiral arrangement of the pharmacophores. As an improvement, a chirality-sensitive flexibility (CSF) descriptor is now introduced, which is based on the distance between a pharmacophore point and a plane defined by three pharmacophore points. The performance of the CSF descriptor was tested on two active series: 37 endomorphin analogues with opiate activity and 38 PGF2alpha analogues with antinidatory activity. The newly devised descriptor resulted in improved QSAR models in terms of both prediction accuracy and precision of the chiral geometric features of the predicted active conformations.
Using Mixed Distribution for Modeling End-to-End Delay Characteristics (2005)

An end-to-end round trip time (RTT) is one of the most important communication characteristics for Internet applications. In order to meet the quality of service (QoS) for applications such as streaming services, it is important to understand and predict the delay characteristic accurately. Because characteristics of the packet transmission delay in the Internet vary strongly related to the time-dependent the condition of network. Especially, it is obvious that two or more factors may interfere in observed delay characteristics. We express these delay characteristics by using the mixture of two or more probability distributions (especially normal distribution), not by single distribution. By investigation the factor which infects the delay distribution, we presume the events that occur in network from the delay characteristic obtained by the observation in the end host.
Microstructural and conductivity comparison of Ag films grown on amorphous TiO2 and polycrystalline ZnO (2001)

8 nm thick Ag films were sputter deposited onto amorphous TiO{sub 2} underlayers 25 nm thick, and also amorphous TiO{sub 2} (25 nm)/ZnO (5 nm) multiunderlayers. The substrates were back-etched Si with a 50 nm thick LPCVD Si{sub 3}N{sub 4} electron transparent membrane. The ZnO, sputtered onto amorphous TiO{sub 2}, formed a continuous layer with a grain size of 5 nm in diameter, on the order of the film thickness. There are several microstructural differences in the Ag dependent on the underlayers, revealed by TEM. First a strong {l_brace}0001{r_brace} ZnO to {l_brace}111{r_brace} Ag fibre-texture relationship exists. On TiO{sub 2} the Ag microstructure shows many abnormal grains whose average diameter is about 60-80 nm, whereas the films on ZnO show few abnormal grains. The background matrix of normal grains on the TiO{sub 2} is roughly 15 nm, while the normal grain size on the ZnO is about 25 nm. Electron diffraction patterns show that the film on ZnO has a strong {l_brace}111{r_brace} orientation, and dark field images with this diffraction condition have a grain size of about 30 nm. In a region near the center of the TEM grid where there is the greatest local heating during deposition, Ag films grown on amorphous TiO{sub 2} are discontinuous, whereas on ZnO, the film is continuous. When films 8 nm films are grown on solid glass substrates, those with ZnO underlayers have sheet resistances of 5.68 {Omega}/, whereas those on TiO{sub 2} are 7.56 {Omega}/, and when 16 nm thick, the corresponding sheet resistances are 2.7 {Omega}/ and 3.3 {Omega}/. The conductivity difference is very repeatable. The improved conductivity is thought to be a combined effect of reduced grain boundary area per unit volume, the predominance of low grain boundary resistivity Coincidence Site Lattice boundaries from the Ag {l_brace}111{r_brace} orientation, and Ag planarization on ZnO resulting in less groove formation on deposition, concluded from atomic force microscopy.
Effectiveness of an educational and physical program in reducing accompanying symptoms in subjects with head and neck pain: a workplace controlled trial (2011)

The objective of this study is to evaluate the effectiveness of an educational and physical program in reducing behavioral or somatic symptoms along with headache, neck and shoulder pain in a working community. A controlled, non-randomized trial was carried out in a working community and 384 employees were enrolled and divided into a study group (Group 1) and a control group (Group 2). The Group 1 received a physical and educational intervention, consisting of relaxation and posture exercises and the use of visual feedback. After 6 months, the intervention was administered to the Group 2. Both groups were then followed for an additional 6 months until the end of the trial. The presence of accompanying symptoms was investigated with a semi-structured interview using a checklist of 20 items, along with headache, neck, and shoulder pain parameters and the prevalence of generalized anxiety disorder and depression, in three clinical examinations at baseline, after 6 months and after 12 months. For each symptom, as well as the presence of any type of symptom, the differences between groups in the prevalence at the clinical examinations following the baseline were evaluated by applying logistic models. After 6 months, the probability of the presence of any type of symptom was significantly lower in the Group 1 (OR 0.69, 95% CI 0.56-0.85) with respect to the Group 2. After 12 months, the pooled estimation did not show any significant difference of symptom prevalence between groups (OR 0.80, 95% CI 0.64-1.00). In conclusion, this is the first longitudinal study relative to accompanying symptoms. Its results suggest the effectiveness of this cognitive program in reducing the burden of physical and psychiatric complaints in a large, working population.
Global solution of anisotropic Quasi-Geostrophic Equations in Sobolev Space (2021)

In \cite{YZ}, the author proved the global existence of the two-dimensional anisotropic quasi-geostrophic equations with condition on the parameters $α,$ $β$ in the Sobolev spaces $H^s( \R^2)$; $s\geq 2$. In this paper, we show that this equations has a global solution in the spaces $H^s(\R^2)$, where $\max\{2-2α,2-2β\}&lt; s&lt;2$, with additional condition over $α$ and $β$. The proof is based on the Gevrey-class regularity of the solution in neighborhood of zero.
Declarative Logic Programming with Primitive Recursive Relations on Lists (1996)

In a previous paper we introduced a system of recursion operators for formulating pure logic programs, dispensing with explicit recursions. The recursion operators, some of which are similar to higher-order functions known from functional programming, take the form of quasi-higher order predicates. In this paper we identify a comprehensive class of logic programs called primitive recursive relations over lists (including primitive recursive functions) using the so called fold recursion operators. We formulate and prove a duality theorem connecting our relational fold operators. We show how correct well-moded procedural interpretations using any fixed computation rule can be obtained from a declarative logic program. This is accomplished in a principled manner by a simplified data flow analysis enabled by the recursion operator formulation and the duality theorem. The recursion operators are handled in ordinary clauses by means of established metalogic programming techniques. Keywords:...
Statistical analysis of digital image fingerprinting based on random projections (2011)

Abstract—Digital fingerprints have recently received a lot of interest in multimedia applications due to their low dimensionality and security/privacy preserving capabilities. In digital fingerprint extraction, random projections play an important role due to their approximate distance preserving property. This paper is dedicated to the analysis of the statistical properties of digital fingerprints obtained based on random projections. In particular, we were able to demonstrate that this sort of mapping guarantees approximate decorrelation of its output with high probability. I.
Ca 2+ modulation of volume‐regulated anion channels: evidence for colocalization with store‐operated channels (2001)

Ca2+ regulation of Cl- current induced by cell swelling (I(CI,swell)) in response to hypotonicity was studied in human prostate cancer epithelial cells (LNCaP) by using the patch-clamp technique. Increase of global intracellular Ca2+ ([Ca2+]in) to 1 mM as well as variations of the extracellular Ca2+ ([Ca2+]out) in the 0 to 10 mM range did not affect time course of the development, maximal amplitude, rectification properties, and kinetics of I(CI,swell). However, the presence of 0.1 mM thapsigargin (TG), an inhibitor of endoplasmic reticulum (ER) Ca2+ pump, resulted in a more than 50% inhibition of ICI,swell. The blockade of plasma membrane store-operated channels (SOCs), activated in the presence of TG, by 2 mM Ni2+ prevented TG-conferred I(CI,swell) inhibition by extracellular Ca2+. In the presence of TG and Ca2+, the cells failed to exhibit regulatory volume decrease. We conclude that interaction between volume-regulated anion channels (VRACs) carrying I(CI,swell) and Ca2+ occurs in the microdomains from the inner surface of the membrane that are not accessible to the changes in [Ca2+]in, but can be readily reached by Ca2+ entering the cell via plasma membrane, especially through SOCs. Preferred access of SOC-transported Ca2+ to VRAC suggests colocalization of these channels in the cell membrane.
A Markovian model for mobile cellular networks with QoS differentiation (2008)

This paper presents a realistic and accurate analytical model to dimension mobile cellular networks with QoS differentiation. QoS per applicative flow is commonly defined in GPRS/EDGE or 3G systems where streaming applications with real time properties and elastic data applications have to share radio resources. The need for accurate and fast-computing tools is of primary importance to tackle complex and exhaustive dimensioning issues. In this paper, we present a generic QoS analytical model developed in the context of EDGE networks but that can be adapted to a different technology. We develop a Markovian model that takes into account the QoS differentiation between real time and non-real time classes and gives expressions for all the required performance parameters. We compare our model with simulation and show its accuracy.
Using resistance and resilience concepts to reduce impacts of invasive annual grasses and altered fire regimes on the sagebrush ecosystem and greater sage-grouse: A strategic multi-scale approach (2014)

This Report provides a strategic approach for conservation of sagebrush ecosystems and Greater Sage- Grouse (sage-grouse) that focuses specifically on habitat threats caused by invasive annual grasses and altered fire regimes. It uses information on factors that influence (1) sagebrush ecosystem resilience to disturbance and resistance to invasive annual grasses and (2) distribution, relative abundance, and persistence of sage-grouse populations to develop management strategies at both landscape and site scales. A sage-grouse habitat matrix links relative resilience and resistance of sagebrush ecosystems with sage-grouse habitat requirements for landscape cover of sagebrush to help decision makers assess risks and determine appropriate management strategies at landscape scales. Focal areas for management are assessed by overlaying matrix components with sage-grouse Priority Areas for Conservation (PACs), breeding bird densities, and specific habitat threats. Decision tools are discussed for determining the suitability of focal areas for treatment and the most appropriate management treatments.
Production and Characterization of Polyhydroxyalkanoates from Wastewater via Mixed Microbial Cultures and Microalgae (2022)

In the context of circular economy and sustainable production of materials, this project investigated the feasibility of producing sustainable polyhydroxyalkanoates (PHA) from microalgae and sludge used in the treatment of municipal wastewater. The overall process was studied looking at the main steps: microalgae production, fermentation of the biomass, production and characterization of the PHAs. It was possible to obtain blends of hydroxybutyrate-hydroxyvalerate copolymers with high molecular weights and different compositions depending on the nature of the feedstock (mixed volatile fatty acids). In some cases, almost completely amorphous PHA materials were obtained, suggesting a potential diversification of uses and applications.
CT synthesis from MR images for orthopedic applications in the lower arm using a conditional generative adversarial network (2019)

Purpose: To assess the feasibility of deep learning-based high resolution synthetic CT generation from MRI scans of the lower arm for orthopedic applications. Methods: A conditional Generative Adversarial Network was trained to synthesize CT images from multi-echo MR images. A training set of MRI and CT scans of 9 ex vivo lower arms was acquired and the CT images were registered to the MRI images. Three-fold cross-validation was applied to generate independent results for the entire dataset. The synthetic CT images were quantitatively evaluated with the mean absolute error metric, and Dice similarity and surface to surface distance on cortical bone segmentations. Results: The mean absolute error was 63.5 HU on the overall tissue volume and 144.2 HU on the cortical bone. The mean Dice similarity of the cortical bone segmentations was 0.86. The average surface to surface distance between bone on real and synthetic CT was 0.48 mm. Qualitatively, the synthetic CT images corresponded well with the real CT scans and partially maintained high resolution structures in the trabecular bone. The bone segmentations on synthetic CT images showed some false positives on tendons, but the general shape of the bone was accurately reconstructed. Conclusions: This study demonstrates that high quality synthetic CT can be generated from MRI scans of the lower arm. The good correspondence of the bone segmentations demonstrates that synthetic CT could be competitive with real CT in applications that depend on such segmentations, such as planning of orthopedic surgery and 3D printing.
Clinical image processing engine (2009)

Our group provides clinical image processing services to various institutes at NIH. We develop or adapt image processing programs for a variety of applications. However, each program requires a human operator to select a specific set of images and execute the program, as well as store the results appropriately for later use. To improve efficiency, we design a parallelized clinical image processing engine (CIPE) to streamline and parallelize our service. The engine takes DICOM images from a PACS server, sorts and distributes the images to different applications, multithreads the execution of applications, and collects results from the applications. The engine consists of four modules: a listener, a router, a job manager and a data manager. A template filter in XML format is defined to specify the image specification for each application. A MySQL database is created to store and manage the incoming DICOM images and application results. The engine achieves two important goals: reduce the amount of time and manpower required to process medical images, and reduce the turnaround time for responding. We tested our engine on three different applications with 12 datasets and demonstrated that the engine improved the efficiency dramatically.
CrossRoads: Seamless VM mobility across data centers through software defined networking (2012)

Most enterprises today run their applications on virtual machines (VMs). VM mobility - both live and offline, can provide enormous flexibility and also bring down OPEX (Operational Expenditure) costs. However, both live and offline migration of VMs is still limited to within a local network because of the complexities associated with cross subnet live and offline migration. These complexities mainly arise from the hierarchical addressing used by various layer 3 routing protocols. For cross data center VM mobility, virtualization vendors require that the network configuration of the new data center where a VM migrates must be similar to that of the old data center. This severely restricts wide spread use of VM migration across data center networks. For offline migration, the above limitations can be overcome by reconfiguring IP addresses for the migrated VMs. However, even this effort is non-trivial and time consuming as these IP addresses are embedded in various configuration files inside these VMs. As enterprises grow and new data centers emerge in different geographic locations, there is a need to interconnect these data centers in a way that allows seamless VM mobility. In this context, we present CrossRoads - a network fabric that provides layer agnostic and seamless live and offline VM mobility across multiple data centers. We leverage software defined networking and implement an OpenFlow based prototype of CrossRoads. CrossRoads extends the idea of location independence based on pseudo addresses proposed in recent research to work with a control plane overlay of OpenFlow network controllers in various data centers. We evaluate CrossRoads on an innovative testbed that leverages nested virtualization to emulate two data centers. Our results confirm that CrossRoads has negligible performance overhead as compared to a Default layer 2 network - its average performance was no worse than 2.3% as compared to Default fabric across all experiments. In some experiments, it even outperformed the Default by up to 30%.