gebhart/patrepeval huggingface dataset:
Quantifying Molecular Bias in DNA Data Storage (2019)

DNA has recently emerged as an attractive medium for future digital data storage because of its extremely high information density and potential longevity. Recent work has shown promising results in developing proof-of-principle prototype systems. However, very uneven (biased) sequencing coverage distributions have been reported, which indicates inefficiencies in the storage process and points to optimization opportunities. These deviations from the average coverage in oligonucleotide copy distribution result in sequence drop-out and make error-free data retrieval from DNA more challenging. The uneven copy distribution was believed to stem from the underlying molecular processes, but the interplay between these molecular processes and the copy number distribution has been poorly understood until now. In this paper, we use millions of unique sequences from a DNA-based digital data archival system to study the oligonucleotide copy unevenness problem and show that two important sources of bias are the synthesis process and the Polymerase Chain Reaction (PCR) process. By mapping the sequencing coverage of a large complex oligonucleotide pool back to its spatial distribution on the synthesis chip, we find that significant bias comes from array-based oligonucleotide synthesis. We also find that PCR stochasticity is another main driver of oligonucleotide copy variation. Based on these findings, we develop a statistical model for each molecular process as well as the overall process and compare the predicted bias with our experimental data. We further use our model to explore the trade-offs between synthesis bias, storage physical density and sequencing redundancy, providing insights for engineering efficient, robust DNA data storage systems.
A Novel Method for High-Power Thermal Vacuum Testing of Satellite Payloads Using Pickup Horns (2007)

This paper presents the development of a novel method for high-power thermal vacuum (TVAC) testing of satellite payloads using pickup horns (PUH). It describes the design, manufacture, and qualification results for a Ku-band pickup horn, followed by high-power thermal vacuum test results of a Ku-band satellite for fixed satellite service. Based on the successful demonstration of this method, a generic pickup horn (GPUH) - with improved performance over a large bandwidth, covering 7.0 GHz to 21.0 GHz - was developed for testing of X-band, Ku-band, and Ka-band satellite payloads. Detailed design and qualification aspects of the generic pickup horn are addressed, including measured results. This method has been successfully employed for high-power thermal vacuum testing of three different satellites at Lockheed Martin Commercial Space Systems (LMCSS), and is the planned testing method for all future payloads.
Exploiting accelerated aging effect for on-line configurability and hardware tracking (2017)

Conventional CMOS technology lacks an efficient way of realizing reconfigurability, which is a highly desired feature for applications such as hardware tracking for security. On the other hand, the traditional “undesirable” aging effect has presented a non-volatile “memory” to the CMOS chip. This paper exploits the aging effects in standard CMOS to enable non-volatile configurability to the chip for application of hardware tracking. A novel accelerated aging circuit is developed to shorten the required stress time to a few seconds of operation. Due to the significant challenges posed by process variation in advanced CMOS technology, a novel stochastic processing methodology is proposed to significantly reduce the failure rate of the tracking and detection. Combining both circuits and system level acceleration, the work of chip usage tracking can be realized within seconds of usage in contrast with days of operation from previously reported aging monitor. The design was implemented and simulated in 45nm CMOS technology with less than 25μW power consumption and compact sizes for easy insertion as a silicon IP using only core transistors. The robustness of the proposed stochastic processing technique has been verified using transistor level Monte-Carlo simulation. Compared with existing aging monitors, the proposed techniques accelerate the process by thousands of times enabling the desired online configurability.
TWO-DIMENSIONAL-ORIENTED LINEAR DISCRIMINANT ANALYSIS FOR FACE RECOGNITION (2006)

Abstract In this paper, a new statistical projection-based method called Two-Dimensional- Oriented Linear Discriminant Analysis (2DO-LDA) is presented. While in the Fisherfaces method the 2D image matrices are first transformed into 1D vectors by merging their rows of pixels, 2DO-LDA is directly applied on matrices, as 2D-PCA. Within and between-class image covariance matrices are generalized, and 2DO-LDA aims at finding a projection space jointly maximizing the second and minimizing the first by considering a generalized Fisher criterion defined on image matrices. A series of experiments was performed on various face image databases in order to evaluate and compare the effectiveness and robustness of 2DO-LDA to 2D-PCA and the Fisherfaces method. The experimental results indicate that 2DO-LDA is more efficient than both 2D-PCA and LDA when dealing with variations in lighting conditions, facial expression and head pose.
The Movable Type Method Applied to Protein–Ligand Binding (2013)

Accurately computing the free energy for biological processes like protein folding or protein-ligand association remains a challenging problem. Both describing the complex intermolecular forces involved and sampling the requisite configuration space make understanding these processes innately difficult. Herein, we address the sampling problem using a novel methodology we term "movable type". Conceptually it can be understood by analogy with the evolution of printing and, hence, the name movable type. For example, a common approach to the study of protein-ligand complexation involves taking a database of intact drug-like molecules and exhaustively docking them into a binding pocket. This is reminiscent of early woodblock printing where each page had to be laboriously created prior to printing a book. However, printing evolved to an approach where a database of symbols (letters, numerals, etc.) was created and then assembled using a movable type system, which allowed for the creation of all possible combinations of symbols on a given page, thereby, revolutionizing the dissemination of knowledge. Our movable type (MT) method involves the identification of all atom pairs seen in protein-ligand complexes and then creating two databases: one with their associated pairwise distant dependent energies and another associated with the probability of how these pairs can combine in terms of bonds, angles, dihedrals and non-bonded interactions. Combining these two databases coupled with the principles of statistical mechanics allows us to accurately estimate binding free energies as well as the pose of a ligand in a receptor. This method, by its mathematical construction, samples all of configuration space of a selected region (the protein active site here) in one shot without resorting to brute force sampling schemes involving Monte Carlo, genetic algorithms or molecular dynamics simulations making the methodology extremely efficient. Importantly, this method explores the free energy surface eliminating the need to estimate the enthalpy and entropy components individually. Finally, low free energy structures can be obtained via a free energy minimization procedure yielding all low free energy poses on a given free energy surface. Besides revolutionizing the protein-ligand docking and scoring problem this approach can be utilized in a wide range of applications in computational biology which involve the computation of free energies for systems with extensive phase spaces including protein folding, protein-protein docking and protein design.
Determination of Acid and Neutral Cannabinoids in Extracts of Different Strains of Cannabis sativa Using GC-FID (2017)

Cannabis (<i>Cannabis sativa</i> L.) is an annual herbaceous plant that belongs to the family Cannabaceae. <i>Trans</i>-Δ<sup>9</sup>-tetrahydrocannabinol (Δ<sup>9</sup>-THC) and cannabidiol (CBD) are the two major phytocannabinoids accounting for over 40% of the cannabis plant extracts, depending on the variety. At the University of Mississippi, different strains of <i>C. sativa,</i> with different concentration ratios of CBD and Δ<sup>9</sup>-THC, have been tissue cultured via micropropagation and cultivated. A GC-FID method has been developed and validated for the qualitative and quantitative analysis of acid and neutral cannabinoids in <i>C. sativa</i> extracts. The method involves trimethyl silyl derivatization of the extracts. These cannabinoids include tetrahydrocannabivarian, CBD, cannabichromene, <i>trans</i>-Δ<sup>8</sup>-tetrahydrocannabinol, Δ<sup>9</sup>-THC, cannabigerol, cannabinol, cannabidiolic acid, cannabigerolic acid, and Δ<sup>9</sup>-tetrahydrocannabinolic acid-A. The concentration-response relationship of the method indicated a linear relationship between the concentration and peak area ratio with R<sup>2</sup> > 0.999 for all 10 cannabinoids. The precision and accuracy of the method were found to be ≤ 15% and ± 5%, respectively. The limit of detection range was 0.11 - 0.19 µg/mL, and the limit of quantitation was 0.34 - 0.56 µg/mL for all 10 cannabinoids. The developed method is simple, sensitive, reproducible, and suitable for the detection and quantitation of acidic and neutral cannabinoids in different extracts of cannabis varieties. The method was applied to the analysis of these cannabinoids in different parts of the micropropagated cannabis plants (buds, leaves, roots, and stems).
Deep-tissue Fluorescence Imaging using Ultrasound-encoded Digitally Time-reversed Light (2012)

Biological tissues significantly scatter light, preventing fluorescence imaging beyond 1 mm deep. By digitally time-reversing ultrasound-encoded light, we achieve high resolution fluorescence imaging at an unprecedented depth of 2.5 mm in scattering biological tissues.
Differential Protection of Cry1Fa Toxin against Spodoptera frugiperda Larval Gut Proteases by Cadherin Orthologs Correlates with Increased Synergism (2011)

The Cry proteins produced by Bacillus thuringiensis (Bt) are the most widely used biopesticides effective against a range of crop pests and disease vectors. Like chemical pesticides, development of resistance is the primary threat to the long-term efficacy of Bt toxins. Recently discovered cadherin-based Bt Cry synergists showed the potential to augment resistance management by improving efficacy of Cry toxins. However, the mode of action of Bt Cry synergists is thus far unclear. Here we elucidate the mechanism of cadherin-based Cry toxin synergism utilizing two cadherin peptides, Spodoptera frugiperda Cad (SfCad) and Manduca sexta Cad (MsCad), which differentially enhance Cry1Fa toxicity to Spodoptera frugiperda neonates. We show that differential SfCad- and MsCad-mediated protection of Cry1Fa toxin in the Spodoptera frugiperda midgut correlates with differential Cry1Fa toxicity enhancement. Both peptides exhibited high affinity for Cry1Fa toxin and an increased rate of Cry1Fa-induced pore formation in S. frugiperda. However, only SfCad bound the S. frugiperda brush border membrane vesicle and more effectively prolonged the stability of Cry1Fa toxin in the gut, explaining higher Cry1Fa enhancement by this peptide. This study shows that cadherin fragments may enhance B. thuringiensis toxicity by at least two different mechanisms or a combination thereof: (i) protection of Cry toxin from protease degradation in the insect midgut and (ii) enhancement of pore-forming ability of Cry toxin.
A high-quality multirate real-time CELP coder (1992)

The design and implementation of a real-time CELP coder for mobile communication applications are discussed. To realize a single-chip implementation, several tradeoffs were made without compromising speech quality. In addition, techniques that make the coder more robust under a variety of channel conditions are discussed. The real-time coder can be operated at different bit rates (8, 6.8, 4.6 kb/s) by simply changing the frame update rates. The speech quality was evaluated through a formal listening test, and it was found that this coder compares favorably with other (standardized) coders operating at similar or higher rates.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
A comparison of neural network feature transforms for speaker diarization (2015)

Speaker diarization finds contiguous speaker segments in an audio stream and clusters them by speaker identity, without using a-priori knowledge about the number of speakers or enrollment data. Diarization typically clusters speech segments based on short-term spectral features. In prior work, we showed that neural networks can serve as discriminative feature transformers for diarization by training them to perform same/different speaker comparisons on speech segments, yielding improved diarization accuracy when combined with standard MFCC-based models. In this work, we explore a wider range of neural network architectures for feature transformation, by adding additional layers and nonlinearities, and by varying the objective function during training. We find that the original speaker comparison netwo rk can be improved by adding a nonlinear transform layer, and that further gains are possible by training the network to perform speaker classification rather than comparison. Overal l we achieve relative reductions in speaker error between 18% and 34% on a variety of test data from the AMI, ICSI, and NIST-RT corpora.
A Highly Conserved gp120 Inner Domain Residue Modulates Env Conformation and Trimer Stability (2016)

Previous studies have shown that highly conserved residues in the inner domain of gp120 are required for HIV-1 envelope glycoprotein (Env) transitions to the CD4-bound conformation (A. Finzi, S. H. Xiang, B. Pacheco, L. Wang, J. Haight, et al., Mol Cell 37:656-667, 2010, http://dx.doi.org/10.1016/j.molcel.2010.02.012; A. Desormeaux, M. Coutu, H. Medjahed, B. Pacheco, A. Herschhorn, et al., J Virol 87:2549-2562, 2013, http://dx.doi.org/10.1128/JVI.03104-12). Moreover, W69, a highly conserved residue located at the interface between layer 1 and layer 2 of the inner domain, was recently shown to be important for efficient Env recognition by CD4-induced (CD4i) antibodies capable of potent antibody-dependent cellular cytotoxicity (W. D. Tolbert, N. Gohain, M. Veillette, J. P. Chapleau, C. Orlandi, et al., 2016, Structure 24:697-709, http://dx.doi.org/10.1016/j.str.2016.03.005; S. Ding, M. Veillette, M. Coutu, J. Prevost, L. Scharf, et al., 2016, J Virol 90:2127-2134, http://dx.doi.org/10.1128/JVI.02779-15). We evaluated the contribution of the hydrophobicity of W69 to conformational changes of Env by replacing it with a series of residues with aliphatic or aromatic side chains of decreasing chain length. We have found that the hydrophobicity of residue 69 is important for Env processing, CD4 binding, and its transition to the CD4-bound conformation. The most deleterious effect was observed when W69 was replaced with alanine or glycine residues. However, the functions lost due to W69 mutations could be progressively restored with amino acids of increasing aliphatic chain length and fully recovered with residues bearing an aromatic ring. Interestingly, poor CD4 binding of W69A could be fully restored by introducing a compensatory mutation within layer 2 (S115W). Structural studies of HIV-1 gp120 coree W69A/S115W mutant bound to the CD4 peptide mimetic M48U1 and Fab of anti-cluster A antibody N60-i3 revealed no perturbations to the overall structure of the double mutant compared to the wild-type protein but identified higher mobility within the interface between layer 1 and layer 2, the bridging sheet region, and the CD4 binding site.IMPORTANCE HIV-1 Env transitions to the CD4-bound conformation are required for viral entry. Previous studies identified a highly conserved residue of the inner domain, W69, as being involved in these conformational transitions (A. Finzi, S. H. Xiang, B. Pacheco, L. Wang, J. Haight, et al., Mol Cell 37:656-667, 2010, http://dx.doi.org/10.1016/j.molcel.2010.02.012). Here, we show that W69, located at the interface between gp120 and gp41 in the PGT151-bound trimer, plays a critical role in the interprotomer signaling induced by CD4 binding. This new information might be useful in immunogen design.
Defining the role of corticotropin releasing factor binding protein in alcohol consumption (2016)

The corticotropin releasing factor (CRF) exerts its effects by acting on its receptors and on the binding protein (CRFBP), and has been implicated in alcohol use disorder (AUD). Therefore, identification of the exact contribution of each protein that mediates CRF effects is necessary to design effective therapeutic strategies for AUD. A series of in vitro/in vivo experiments across different species were performed to define the biological discrete role of CRFBP in AUD. First, to establish the CRFBP role in receptor signaling, we developed a novel chimeric cell-based assay and showed that CFRBP full length can stably be expressed on the plasma membrane. We discovered that only CRFBP(10 kD) fragment is able to potentiate CRF-intracellular Ca<sup>2+</sup> release. We provide evidence that CRHBP gene loss increased ethanol consumption in mice. Then, we demonstrate that selective reduction of CRHBP expression in the center nucleus of the amygdala (CeA) decreases ethanol consumption in ethanol-dependent rats. CRFBP amygdalar downregulation, however, does not attenuate yohimbine-induced ethanol self-administration. This effect was associated with decreased hemodynamic brain activity in the CRFBP-downregulated CeA and increased hemodynamic activity in the caudate putamen during yohimbine administration. Finally, in alcohol-dependent patients, genetic variants related to the CRFBP(10 kD) fragment were associated with greater risk for alcoholism and anxiety, while other genetic variants were associated with reduced risk for anxiety. Taken together, our data provide evidence that CRFBP may possess both inhibitory and excitatory roles and may represent a novel pharmacological target for the treatment of AUD.
Detection of human antibodies against Plasmodium falciparum sporozoites using synthetic peptides (1987)

A large peptide consisting of about 40 (Asn-Ala-Asn-Pro) repeats of Plasmodium falciparum circumsporozoite protein, (NANP)40, was synthesized. It was recognized specifically by monoclonal antibodies produced against P. falciparum sporozoites. Moreover, this peptide strongly inhibited the binding of such monoclonal antibodies to antigens present in a sporozoite extract. The (NANP)40 peptide was employed without any carrier to develop an enzyme-linked immunosorbent assay to detect sporozoite-specific serum antibodies arising after natural malaria infections. Antibodies were detected in a high percentage (43.1%) of European patients suffering from acute P. falciparum malaria and in Africans living in an area of Gabon endemic for malaria. In the latter group, the frequency of antisporozoite antibodies increased with age, reaching 65.9% in individuals more than 40 years old. There was a significant correlation between the results obtained with an immunofluorescence assay with glutaraldehyde-fixed sporozoites and those obtained by enzyme-linked immunosorbent assay with (NANP)40. Therefore, such synthetic peptides representing the repetitive epitope of P. falciparum circumsporozoite protein can be used for the detection of antisporozoite antibodies and for the epidemiological studies required to obtain base-line data concerning the immune status of individuals before their participation in a sporozoite vaccine trial.
Cross sections required for FMIT dosimetry (1980)

The Fusion Materials Irradiation Test (FMIT) facility, currently under construction, is designed to produce a high flux of high energy neutrons for irradiation effects experiments on fusion reactor materials. Characterization of the flux-fluence-spectrum in this rapidly varying neutron field requires adaptation and extension of currently available dosimetry techniques. This characterization will be carried out by a combination of active, passive, and calculational dosimetry. The goal is to provide the experimenter with accurate neutron flux-fluence-spectra at all positions in the test cell. Plans have been completed for a number of experimental dosimetry stations and provision for these facilities has been incorporated into the FMIT design. Overall needs of the FMIT irradiation damage program delineate goal accuracies for dosimetry that, in turn, create new requirements for high energy neutron cross section data. Recommendations based on these needs have been derived for required cross section data and accuracies.
Genetically Modified L3,7 and L2 Lipooligosaccharides from <i>Neisseria meningitidis</i> Serogroup B Confer a Broad Cross-Bactericidal Response (2009)

Currently available Neisseria meningitidis serogroup B (MenB) vaccines are based on outer membrane vesicles (OMVs) that are obtained from wild-type strains. They are purified with the aim of decreasing the lipooligosaccharide (LOS) content and hence reduce the reactogenicity of the vaccine even though LOS is a potential protective antigen. In <2-year-old children, these MenB vaccines confer protection only against strains expressing homologous PorA, a major and variable outer membrane protein. Our objective was to develop a safe LOS-based vaccine against MenB. To this end, we used modified porA knockout strains expressing genetically detoxified (msbB gene-deleted) L2 and L3,7 LOSs, allowing the production of LOS-enriched OMVs. The vaccine-induced antibodies were found to be bactericidal against nearly all invasive strains, irrespective of capsular serogroup. In addition, we have also demonstrated that LOS lacking the terminal galactose (with a lgtB mutation; truncated L3 LOS), but not LOS produced without the galE gene, induced a bactericidal antibody response in mice similar to that seen for LOS containing the full lacto-N-neotetraose (L3,7 LOS). In conclusion, a bivalent detoxified LOS OMV-based vaccine demonstrated the potential to afford a broad cross-protection against meningococcal disease.
Parallel adaptive decision feedback equalizers (1993)

Several algorithms for parallel implementation of adaptive decision feedback equalizers (DFEs) are proposed. The first is a double-row DFE algorithm that outperforms previous approaches. Under the no-error-propagation assumption, the algorithm will perform exactly like a serially adapting DFE. The multiplication complexity of the double-row DFE algorithm is of the same order as that of the parallel DFE algorithm and the extended least-mean-square (LMS) method. The previous algorithms and the double-row DFE algorithm may become impractical to implement due to their large computational complexity, so three additional parallel implementations of the DFE, which lead to considerable hardware savings and avoid the coding loss of the former approaches, are presented. The different algorithms are compared on the basis of convergence analysis and simulation results.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Supporting soft real-time tasks in the xen hypervisor (2010)

Virtualization technology enables server consolidation and has given an impetus to low-cost green data centers. However, current hypervisors do not provide adequate support for real-time applications, and this has limited the adoption of virtualization in some domains. Soft real-time applications, such as media-based ones, are impeded by components of virtualization including low-performance virtualization I/O, increased scheduling latency, and shared-cache contention. The virtual machine scheduler is central to all these issues. The goal in this paper is to adapt the virtual machine scheduler to be more soft-real-time friendly.