gebhart/patrepeval huggingface dataset:
Native Capillary Isoelectric Focusing for the Separation of Protein Complex Isoforms and Subcomplexes (2010)

Here we report the use of capillary isoelectric focusing under native conditions for the separation of protein complex isoforms and subcomplexes. Using biologically relevant HIS-tag and FLAG-tag purified protein complexes, we demonstrate the separations of protein complex isoforms of the mammalian target of rapamycin complex (mTORC1 and 2) and the subcomplexes and different phosphorylation states of the Dam1 complex. The high efficiency capillary isoelectric focusing separation allowed for resolution of protein complexes and subcomplexes similar in size and biochemical composition. By performing separations with native buffers and reduced temperature (15 degrees C) we were able to maintain the complex integrity of the more thermolabile mTORC2 during isoelectric focusing and detection (<45 min). Increasing the separation temperature allowed us to monitor dissociation of the Dam1 complex into its subcomplexes (25 degrees C) and eventually its individual protein components (30 degrees C). The separation of two different phosphorylation states of the Dam1 complex, generated from an in vitro kinase assay with Mps1 kinase, was straightforward due to the large pI shift upon multiple phosphorylation events. The separation of the protein complex isoforms of mTORC, on the other hand, required the addition of a small pI range (4-6.5) of ampholytes to improve resolution and stability of the complexes. We show that native capillary isoelectric focusing is a powerful method for the difficult separations of large, similar, unstable protein complexes. This method shows potential for differentiation of protein complex isoform and subcomplex compositions, post-translational modifications, architectures, stabilities, equilibria, and relative abundances under biologically relevant conditions.
Renewable fluid dynamic energy derived from aquatic animal locomotion (2007)

Aquatic animals swimming in isolation and in groups are known to extract energy from the vortices in environmental flows, significantly reducing muscle activity required for locomotion. A model for the vortex dynamics associated with this phenomenon is developed, showing that the energy extraction mechanism can be described by simple criteria governing the kinematics of the vortices relative to the body in the flow. In this way, we need not make direct appeal to the fluid dynamics, which can be more difficult to evaluate than the kinematics. Examples of these principles as exhibited in swimming fish and existing energy conversion devices are described. A benefit of the developed framework is that the potentially infinite-dimensional parameter space of the fluid-structure interaction is reduced to a maximum of eight combinations of three parameters. The model may potentially aid in the design and evaluation of unsteady aero- and hydrodynamic energy conversion systems that surpass the Betz efficiency limit of steady fluid dynamic energy conversion systems.
ChemInform Abstract: Acyclic Nucleotide Analogues. Part 4. Phosphonylmethoxyalkyl and Phosphonylalkyl Derivatives of Adenine. (1989)

Abstract For structure‐activity studies of the antiviral effect in a series of acyclic nucleotides a series of ca. 50 novel members such as (IV), (VI), (VII) or (VIII) is synthesized with variations in the character of the heterocyclic base, the aliphatic side chain and the presence, character and bonding of the phosphonyl group.
ChemInform Abstract: Mono‐ and N1,N7‐Dialkylation of 1,4,7,10‐Tetraazacyclododecane via Silicon Protection. (1995)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Experimental design and investigation of a pin-type reconfigurable clamping system for manufacturing aerospace components (2003)

This paper presents an experimental design and evaluation of a pin-type universal clamping system. The clamping system is designed for holding complex-shaped aerospace components, such as turbine blades, during machining processes. The experimental investigation is performed by comparing the pin-type clamping system with a dedicated clamping system during the machining of aluminium and steel parts. Force signals are monitored during machining. The experimental results are presented and compared with a dedicated clamping system. From the comparison, the performance of the clamping system is discussed. The results provide an evaluation of the designed pin-type clamping systems for machining operations. The results prove that the pin-type clamping system can be reconfigured for machining different complex shaped components with performance comparable with a dedicated clamping system.
Electrical Energy Density and Discharge Characteristics of a Poly(vinylidene fluoride-chlorotrifluoroethylene)Copolymer (2007)

The high electric displacement (D>0.1 C/m <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> ) and breakdown field (600 MV/m) in polyvinylidene fluoride based polymers suggest high electrical energy density in this class of polymers. By defect modifications which reduce or eliminate the remnant polarization in the polymer, a high electrical energy density can indeed be obtained. This paper shows that in properly prepared P(VDF-CTFE) copolymer film capacitors, an electrical energy density ~25 J/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> can be obtained with a breakdown field higher than 600 MV/m. The dielectric and discharge behavior of the polymer films were investigated. The results reveal that there are strong frequency dispersions in both the dielectric and discharge behavior. The dielectric constant decreases with frequency and the discharged energy density is also reduced at shorted discharge time (~1 mus) due to increased ESR for fast discharge. The results indicate the potential of this class of polymers for high energy density capacitors and suggest the need for further tuning of the polymer compositions to reduce the frequency dispersion.
Practical Solutions for Protecting Individual Genomic Privacy (2014)

The increasing availability of genomic data has major implications for personal privacy. The issues raised by genomic privacy reside at the crossroads of medicine, computer science, legislation and public policy. We here describe the design and development of new privacy enhancing technologies that aim to find the optimal balance between usability and privacy of genomic data in clinical care and in biomedical research.
Prediction of Cyberbullying Incidents on the Instagram Social Network (2015)

Cyberbullying is a growing problem affecting more than half of all American teens. The main goal of this paper is to investigate fundamentally new approaches to understand and automatically detect and predict incidents of cyberbullying in Instagram, a media-based mobile social network. In this work, we have collected a sample data set consisting of Instagram images and their associated comments. We then designed a labeling study and employed human contributors at the crowd-sourced CrowdFlower website to label these media sessions for cyberbullying. A detailed analysis of the labeled data is then presented, including a study of relationships between cyberbullying and a host of features such as cyberaggression, profanity, social graph features, temporal commenting behavior, linguistic content, and image content. Using the labeled data, we further design and evaluate the performance of classifiers to automatically detect and pre- dict incidents of cyberbullying and cyberaggression.
Energetic limits to metabolic flexibility: responses of Saccharomyces cerevisiae to glucose–galactose transitions (2009)

Glucose is the favoured carbon source for Saccharomyces cerevisiae, and the Leloir pathway for galactose utilization is only induced in the presence of galactose during glucose-derepressed conditions. The goal of this study was to investigate the dynamics of glucose-galactose transitions. To this end, well-controlled, glucose-limited chemostat cultures were switched to galactose-excess conditions. Surprisingly, galactose was not consumed upon a switch to galactose excess under anaerobic conditions. However, the transcripts of the Leloir pathway were highly increased upon galactose excess under both aerobic and anaerobic conditions. Protein and enzyme-activity assays showed that impaired galactose consumption under anaerobiosis coincided with the absence of the Leloir-pathway proteins. Further results showed that absence of protein synthesis was not caused by glucose-mediated translation inhibition. Analysis of adenosine nucleotide pools revealed a fast decrease of the energy charge after the switch from glucose to galactose under anaerobic conditions. Similar results were obtained when glucose-galactose transitions were analysed under aerobic conditions with a respiratory-deficient strain. It is concluded that under fermentative conditions, the energy charge was too low to allow synthesis of the Leloir proteins. Hence, this study conclusively shows that the intracellular energy status is an important factor in the metabolic flexibility of S. cerevisiae upon changes in its environment.
Systolic IIR filters with bit level pipelining (2003)

A novel bit-level systolic array architecture for implementing first-order IIR filter sections is presented. A latency of only two clock cycles is achieved by using a radix-4 redundant number representation, performing the recursive computation most-significant-digit first, and feeding back each digit of the result as soon as it is available.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A Machine Learning Approach to Optimal Inverse Discrete Cosine Transform (IDCT) Design (2021)

The design of the optimal inverse discrete cosine transform (IDCT) to compensate the quantization error is proposed for effective lossy image compression in this work. The forward and inverse DCTs are designed in pair in current image/video coding standards without taking the quantization effect into account. Yet, the distribution of quantized DCT coefficients deviate from that of original DCT coefficients. This is particularly obvious when the quality factor of JPEG compressed images is small. To address this problem, we first use a set of training images to learn the compound effect of forward DCT, quantization and dequantization in cascade. Then, a new IDCT kernel is learned to reverse the effect of such a pipeline. Experiments are conducted to demonstrate that the advantage of the new method, which has a gain of 0.11-0.30dB over the standard JPEG over a wide range of quality factors.
Chern Classes of Locally Free Sheaves (1998)

The purpose of this chapter is to define Chern classes of locally free sheaves on projective schemes. This theory will be used in the definition of local Chern characters of complexes in Chapter 11. We first define the concept of a sheaf on Proj(A), where A is a graded ring; we define a sheaf to be an equivalence class of graded A-modules, where two modules are equivalent when their restrictions to any open set of Proj(A) are the same (the precise definition is given in Section 1). This is not the usual definition of a sheaf, but the theory is essentially equivalent to that of quasi-coherent sheaves for projective schemes (see Hartshorne). This definition suffices for our purposes, and it makes it easy to prove the important facts that we need. We are particularly interested in locally free sheaves, for which it is possible to define certain intersection classes on the Chow group of Proj(A), called Chern classes, which in some sense measure how far the module is from being free. We describe the theory of Chern classes in this chapter and prove the functorial properties necessary for later applications. In the last section we define the push-forward of a sheaf by a projective map, which will be used in the proof of the local Riemann-Roch formula in Chapter 12.
Fabrication and Closure Development of Nuclear Waste Containers for Storage at the Yucca Mountain, Nevada Repository (1990)

U.S. Congress and the President have determined that the Yucca Mountain site in Nevada is to be characterized to determine its suitability for construction of the first U.S. high-level nuclear waste repository. Work in connection with this site is carried out within the Yucca Mountain Project (YMP). Lawrence Livermore National Laboratory (LLNL) has the responsibility for designing, developing, and projecting the performance of the waste package for the permanent storage of high-level nuclear waste * . Babcock & Wilcox (B&W) is involved with the YMP as a subcontractor to LLNL. B&W's role is to recommend and demonstrate a method for fabricating the metallic waste container and a method for performing the final closure of the container after it has been filed with waste. Various fabrication and closure methods are under consideration for the production of containers. This paper presents progress to date in identifying and evaluating the candidate manufacturing processes.
DNA sequencing from single phage plaques using solid-phase magnetic capture. (1995)

Many operations encountered in molecular cloning are labor-intensive and time-consuming. One case that is often troublesome is the subcloning of cDNA clones from lambda gt11 phage into plasmid vectors. In situations where several clones have been isolated, time could be saved by a means of assessing insert size and sequence unambiguously without subcloning, particularly where degenerate PCR or low-stringency hybridization approaches are taken to identify multiple members of a gene family. We describe a simple and reliable strategy for efficient sequencing of small amounts of lambda phage DNA, lysates or individual phage plaques. The strategy combines the advantages of universal lambda phage primers, rapid air thermal cycling, streptavidin magnetic bead capture of highly purified single-stranded templates and the unparalleled clarity of T7 DNA polymerase sequence. We routinely obtain 350-500 bases of unambiguous sequence from each reaction. It takes only hours from lifting phage plaques to finishing the sequencing reactions. The method provides an alternative to thermal cycle sequencing that has comparable sensitivity and affords sequence data of much higher clarity.
Coating Electrospun Poly(ε-caprolactone) Fibers with Gelatin and Calcium Phosphate and Their Use as Biomimetic Scaffolds for Bone Tissue Engineering (2008)

Electrospinning was employed to fabricate fibrous scaffolds of poly(epsilon-caprolactone) in the form of nonwoven mats. The surfaces of the fibers were then coated with gelatin through layer-by-layer self-assembly, followed by functionalization with a uniform coating of bonelike calcium phosphate by mineralization in the 10 times concentrated simulated body fluid for 2 h. Transmission electron microscopy, water contact angle, and scanning electron microscopy measurements confirmed the presence of gelatin and calcium phosphate coating layers, and X-ray diffraction results suggested that the deposited mineral phase was a mixture of dicalcium phosphate dehydrate (a precursor to apatite) and apatite. It was also demonstrated that the incorporation of gelatin promoted nucleation and growth of calcium phosphate. The porous scaffolds could mimic the structure, composition, and biological function of bone extracellular matrix. It was found that the preosteoblastic MC3T3-E1 cells attached, spread, and proliferated well with a flat morphology on the mineralized scaffolds. The proliferation rate of the cells on the mineralized scaffolds was significantly higher (by 1.9-fold) than that on the pristine fibrous scaffolds after culture for 7 days. These results indicated that the hybrid system containing poly(epsilon-caprolactone), gelatin, and calcium phosphate could serve as a new class of biomimetic scaffolds for bone tissue engineering.
Spatial Organization and Correlations of Cell Nuclei in Brain Tumors (2011)

Accepting the hypothesis that cancers are self-organizing, opportunistic systems, it is crucial to understand the collective behavior of cancer cells in their tumorous heterogeneous environment. In the present paper, we ask the following basic question: Is this self-organization of tumor evolution reflected in the manner in which malignant cells are spatially distributed in their heterogeneous environment? We employ a variety of nontrivial statistical microstructural descriptors that arise in the theory of heterogeneous media to characterize the spatial distributions of the nuclei of both benign brain white matter cells and brain glioma cells as obtained from histological images. These descriptors, which include the pair correlation function, structure factor and various nearest neighbor functions, quantify how pairs of cell nuclei are correlated in space in various ways. We map the centroids of the cell nuclei into point distributions to show that while commonly used local spatial statistics (e.g., cell areas and number of neighboring cells) cannot clearly distinguish spatial correlations in distributions of normal and abnormal cell nuclei, their salient structural features are captured very well by the aforementioned microstructural descriptors. We show that the tumorous cells pack more densely than normal cells and exhibit stronger effective repulsions between any pair of cells. Moreover, we demonstrate that brain gliomas are organized in a collective way rather than randomly on intermediate and large length scales. The existence of nontrivial spatial correlations between the abnormal cells strongly supports the view that cancer is not an unorganized collection of malignant cells but rather a complex emergent integrated system.
Reasoning about Bayesian Network Classifiers (2012)

Bayesian network classifiers are used in many fields, and one common class of classifiers are naive Bayes classifiers. In this paper, we introduce an approach for reasoning about Bayesian network classifiers in which we explicitly convert them into Ordered Decision Diagrams (ODDs), which are then used to reason about the properties of these classifiers. Specifically, we present an algorithm for converting any naive Bayes classifier into an ODD, and we show theoretically and experimentally that this algorithm can give us an ODD that is tractable in size even given an intractable number of instances. Since ODDs are tractable representations of classifiers, our algorithm allows us to efficiently test the equivalence of two naive Bayes classifiers and characterize discrepancies between them. We also show a number of additional results including a count of distinct classifiers that can be induced by changing some CPT in a naive Bayes classifier, and the range of allowable changes to a CPT which keeps the current classifier unchanged.
A new improved collage theorem with applications to multiresolution fractal image coding (2002)

The paper presents an improved collage theorem, valid for a class of signal mappings called affine blockwise average (ABA) mappings. The ABA structure is exploited to form a bound depending on norms of collage error signals at several resolutions. Compared to previously published collage theorems, the new theorem provides a much tighter bound on the maximum distance between the original signal (real world image) and the decoder attractor, given the distance between the original and the "collage" optimized by the encoder. This is achieved without contractivity constraints on the ABA mapping parameters. Finally, an encoding method in which one attempts to minimize the upper bound directly is suggested.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Epstein-Barr virus-associated hemophagocytic syndrome: virological and immunopathological studies (1985)

The virus-associated hemophagocytic syndrome (VAHS) is a disorder characterized by a benign, generalized histiocytic proliferation, with marked hemophagocytosis associated with systemic viral infections. We have studied the virological and immunopathological events occurring in two children experiencing Epstein-Barr VAHS. Neither of the patients had an underlying immunodeficiency and both recovered from their disease and are completely well one year after follow-up. In each patient, evidence for primary Epstein-Barr virus (EBV) infection was documented with a typical humoral immune response, including IgM antibody directed against virus capsid antigen. EBV was demonstrated in lymphoreticular tissues by electron microscopy and molecular hybridization studies. Permissive EBV infection was suggested by the finding of mature virus particles and linear viral DNA in lymphoreticular tissues. Immunopathological studies demonstrated complete effacement of lymph node architecture by a marked proliferation of immunoblasts in patient 1 and infiltration and effacement of the lymph node architecture with benign-appearing histiocytes in patient 2. Atypical lymphocytes characteristic of acute EBV infection were notably absent in the peripheral blood of both patients and cytotoxic T cells, which normally lyse EBV-infected B cells, were also absent from the peripheral circulation. Our observations suggest that EBV-induced VAHS may be the result of an increased virus burden in the face of immunoregulatory cell imbalances.
Different prognostic value of functional right ventricular parameters in arrhythmogenic right ventricular cardiomyopathy (2013)

Purpose: The purpose of this longitudinal multicenter study was to describe the change of RV Fractional Area Change (FAC) and Tricuspid Annulus Plane Systolic Excursion (TAPSE) among other echocardiographic (TTE) parameters during long-term follow-up and to define their prognostic value in a relatively large cohort of patients with Arrhythmogenic Right Ventricular Cardiomyopathy (ARVC). Methods: We investigated the impact of FAC and TAPSE for prediction of Major Adverse Cardiovascular Events (MACE). Patients were recruited at 3 Swiss centers. From this cohort, 70 patients with the diagnosis ARVC according to the 2010 Revised Task Force Criteria (TFC), in whom a Two-Dimensional (2-D) TTE was performed at baseline and who had a follow-up period of at least 3 months, were included in this study. Patients, in whom the diagnosis was made by inclusion of FAC, were excluded in order to avoid interaction bias with disease probability. Results: 37 patients (53%) experienced MACE during a median follow-up period of 5.3 (IQR 1.8-9.8) years. FAC (p=0.032) and TAPSE decreased over time (p=0.041), whereas right ventricular end-diastolic area increased (p=0.029, each vs. baseline). Kaplan-Meier analysis (Figure) revealed a reduced cumulative survival among patients with FAC <23% (p<0.001), TAPSE <17mm (p=0.021), or Right Atrial (RA) short axis/BSA ≥25mm/m2 (p=0.037) at baseline. A reduced FAC constituted the only independent predictor of MACE on multivariate analysis (HR 1.07 per 1% decrease; 95% CI 1.02-1.11; p=0.004). Figure 1. Kaplan-Meier curves Conclusions: This long-term observational data indicates that FAC is the only independent predictor of MACE in ARVC, while TAPSE and dilatation of right-sided cardiac chambers have a lower predictive value. These parameters advocate a role for TTE in risk stratification in ARVC.