gebhart/patrepeval huggingface dataset:
Reactivity of recombinant treponema pallidum (r‐Tp) antigens with anti‐Tp antibodies in human syphilitic sera evaluated by ELISA (1997)

We evaluated the immunoreactivity of recombinant Treponema pallidum (r-Tp) antigens with human sera by indirect enzyme-linked immunoabsorbant assay (ELISA). We expressed antigens with a molecular weight (MW) of 17KDa, 15KDa, 47KDa, and 42KDa, which are believed to be major immunoreactive membrane proteins of Tp cells. The expressed proteins were described by adding the prefix M, S, and G to the corresponding Tp antigens, namely, mature antigens, signal sequence containing antigens, and glutathione s-transferase (GST)-fused antigen in this report. A rather high expression occurred for M47 and S42 proteins in the Escherichia coli system, whereas for M15 and M17 proteins, a poor expression was observed. However, a fairly high expression occurred for G15 and G17. Thus expressed proteins were purified by means of chromatographies to a level of > 95%, and the purified proteins were found to be reactive with TPHA positive serum by Western blotting (WB). An ELISA performed with a serum of 1/1000 dilution using these purified antigens for coating on the solid phase showed that G17 antigen was more effective in detecting syphilis antibodies in human serum than M47, S42, and G15. There was a good consistency between ELISA and TPHA, whereby the cutoff indexes (CI) on ELISA showed a correlation coefficient of 0.7276 in logarithmic TPHA titers. J. Clin. Lab. Anal. 11:315–322, 1997. © 1997 Wiley-Liss, Inc.
Genetic optimization of a hybrid DISS Tx antenna (2004)

Genetic algorithms have been shown to be effective in the design and optimization of many types of antenna. In this paper, we show how genetic algorithm antenna research at the Air Force Research Laboratory (AFRL) has been applied to a real-world problem - the re-design of the DISS transmit antenna. We present a brief background of the problem, describe our optimization goals and constraints, and compare the existing antenna performance to an LPDA-augmented hybrid antenna and a genetically-optimized hybrid antenna.
Efficient and Sustained Gene Expression in Primary T Lymphocytes and Primary and Cultured Tumor Cells Mediated by Adeno-Associated Virus Plasmid DNA Complexed to Cationic Liposomes (1994)

We have used cationic liposomes to facilitate adeno-associated virus (AAV) plasmid transfections of primary and cultured cell types. AAV plasmid DNA complexed with liposomes showed levels of expression several fold higher than those of complexes with standard plasmids. In addition, long-term expression (> 30 days) of the gene, unlike the transient expression demonstrated by typical liposome-mediated transfection with standard plasmids, was observed. Southern analysis of chromosomal DNA further substantiated the hypothesis that the long-term expression was due to the presence of the transgene in the AAV plasmid-transfected group and not in the standard plasmid-transfected group. AAV plasmid-liposome complexes induced levels of transgene expression comparable to those obtained by recombinant AAV transduction. Primary breast, ovarian, and lung tumor cells were transfectable with the AAV plasmid DNA-liposome complexes. Transfected primary and cultured tumor cells were able to express transgene product even after lethal irradiation. High-level gene expression was also observed in freshly isolated CD3+, CD4+, and CD8+ T cells from normal human peripheral blood. Transfection efficiency ranged from 10 to 50% as assessed by intracellular interleukin-2 levels in interleukin-2-transfected cells. The ability to express transgenes in primary tumor and lymphoid cells may be applied toward tumor vaccine studies and protocols which may eventually permit highly specific modulation of the cellular immune response in cancer and AIDS.
Malware Target Recognition of Unknown Threats (2012)

Organizations traditionally use signature-based commercial antivirus products as a frontline defense against malware, but advanced persistent threats craft custom malicious tools to achieve their objectives. Organizations safeguarding sensitive information have difficulty in identifying new malware threats among millions of benign executables using only signature-based antivirus systems. This paper extends a performance-based malware target recognition architecture that currently uses only static heuristic features. Experimental results show that this architectural component achieves an overall test accuracy of 98.5% against a malware set collected from operational environments, while three commercial antivirus products combine for a detection accuracy of only 60% with their most sensitive settings. Implementations of this architecture will enable organizations to self-discover new malware threats, providing enhanced situation awareness for cyberspace operators in hostile threat environments.
Staged low NO sub x premix gas turbine combustor (1990)

This patent describes a staged low NO{sub x} lean premix hot wall method for combusting fuel in a gas turbine combustor. It comprises: inducting a first lean premixture of fuel and compressed air into a first stage of a combustion chamber; igniting and combusting the inducted first premixture of fuel and air within the first stage of the combustion chamber to produce a stream of combustion products exiting the first stage of the combustion chamber; inducting streams of a second premixture of fuel and compressed air into a second stage of the combustion chamber downstream of the first stage from generally opposite directions and colliding the streams in an impact region within the stream of combustion products exiting the first stage of the combustion chamber to produce a divergent intensely turbulent flow emanating from the impact region to define a stirred reactor region within the second stage of the combustion chamber.
L1 (CD171) as a novel biomarker for ovarian and endometrial carcinomas (2004)

The L1 molecule has emerged as a promising new biomarker for the diagnosis and prognosis of human ovarian and endometrial tumors. It was initially described as an adhesion molecule for neural cells but its function on tumor cells is less well known. In this article, the role of L1 in promoting tumor cell adhesion and migration is discussed. The question of how L1 determination in tumor tissue samples, serum and ascites could potentially improve the diagnosis and monitoring of gynecologic tumor patients is also addressed. The presence of L1 in tissue and serum was found to be associated with recurrent disease and short survival, independently of the tumor's histological type. This provides an alternative classification of gynecologic tumors according to their aggressiveness rather than their histology. L1 expression was correlated with disease progression even in patients with Stage I endometrioid-type endometrial tumors, identifying them as high-risk patients on preoperative curettage specimens. Monitoring of soluble L1 during the follow-up period was found to signal disease progression and recurrence before clinical symptoms occur. L1-based diagnosis and prognosis has the potential to contribute to an improved disease management and could represent the basic rationale for novel tailored therapy.
Supramolecular Materials: Multifunctional Supramolecular Hybrid Materials Constructed from Hierarchical Self‐Ordering of In Situ Generated Metal‐Organic Framework (MOF) Nanoparticles (Adv. Mater. 30/2015) (2015)

The supramolecular engineering of a new family of hybrid gels coexisting with metal-organic framework (MOF) nano-particles created in situ is demonstrated by J. C. Tan and co-workers on page 4438. The rapid process of inorganic-organic self-assembly generates a hierarchical fiber network architecture, whose electrical conductivity and mechanical characteristics can be tuned to yield a range of bespoke soft matter with unconventional properties.
High speed memory efficient EBCOT architecture for JPEG2000 (2003)

This paper presents a high speed, memory efficient architecture of embedded block coding with optimized truncation (EBCOT) tier-1 in JPEG2000. By parallel coding all the bitplanes, the state variable memory can be eliminated. The proposed architecture can process 50 M coefficients per second at 100 MHz, which can realtime encode 720p resolution of HDTV picture format at 30 fps.
A novel thiol antioxidant that crosses the blood brain barrier protects dopaminergic neurons in experimental models of Parkinson's disease (2005)

It is believed that oxidative stress (OS) plays an important role in the loss of dopaminergic nigrostriatal neurons in Parkinson's disease (PD) and that treatment with antioxidants might be neuroprotective. However, most currently available antioxidants cannot readily penetrate the blood brain barrier after systemic administration. We now report that AD4, the novel low molecular weight thiol antioxidant and the N-acytel cysteine (NAC) related compound, is capable of penetrating the brain and protects neurons in general and especially dopaminergic cells against various OS-generating neurotoxins in tissue cultures. Moreover, we found that treatment with AD4 markedly decreased the damage of dopaminergic neurons in three experimental models of PD. AD4 suppressed amphetamine-induced rotational behaviour in rats with unilateral 6-OHDA-induced nigral lesion. It attenuated the reduction in striatal dopamine levels in mice treated with 1-methyl-4-phenyl-1,2,3,6,-tetrahydropyridine (MPTP). It also reduced the dopaminergic neuronal loss following chronic intrajugular administration of rotenone in rats. Our findings suggest that AD4 is a novel potential new neuroprotective drug that might be effective at slowing down nigral neuronal degeneration and illness progression in patients with PD.
Detecting preeclampsia with a multiple protein serum test: Assay and algorithm development (2023)

Abstract Background Preeclampsia is a common cause of maternal and neonatal mortality, and to date there is no definitive, diagnostic test available. We aimed to develop a test to detect preeclampsia using biomarkers representing different pathogenic pathways of disease. Methods A multi-stage development process was used to identify, prioritize, and assess performance of the biomarkers. Samples from symptomatic, asymptomatic, and subjects diagnosed with preeclampsia were screened to produce an algorithm with eight proteins and one clinical biomarker in order to report a binary output of “positive” or “negative”. Test performance was reported on a development cohort, and analytical validation was completed for the underlying protein assays. Results The algorithm resulted sensitivity of 90.6% (CI: 83.1%-95.0%), specificity of 78.4% (CI: 73.9%-82.4%), negative predictive value (NPV) of 96.9% (CI: 94.3%-98.4%), and positive predictive value (PPV) of 52.7% (CI: 45.1%-60.2%) for classification of presence or absence of preeclampsia. Conclusion A panel of biomarkers representing different physiological pathways in preeclampsia measured in serum of symptomatic women provides a sensitive binary classification of presence or absence of disease.
Capsular Polysaccharide Synthesis Regions in <i>Klebsiella pneumoniae</i> Serotype K57 and a New Capsular Serotype (2008)

Community-acquired pyogenic liver abscess caused by Klebsiella pneumoniae is an emerging infectious disease. We explored the capsular polysaccharide synthesis (cps) regions of three non-K1, non-K2 K. pneumoniae strains, A1142, A7754, and A1517, from Taiwanese patients experiencing pyogenic liver abscess. Two of the strains, A1142 and A7754, belonged to capsular serotype K57, while the third belonged to a new capsular serotype, different from the previously reported 77 serotypes. Deletion and complementation experiments suggested that a unique K57 gene, a homologue of wzy, was essential for K57 capsular synthesis and confirmed that this gene cluster was a genetic coding region for K57. Compared to K1 and K2 strains, the three strains were all serum sensitive, suggesting that host factors might also be involved in the three patients. PCR using primers from specific genes for K57 was more sensitive and specific than traditional serotyping. The remaining strain, A1517, did not react to the antisera from any of the 77 serotypes, and none of the 77 reference strains reacted to the serum against this strain. Moreover, PCR analyses using various primer pairs from the serotype-specific open reading frames did not reveal cross-reactivity to any of the 77 reference strains, suggesting that this strain likely represents a new capsular type. We conclude that sequences from these two cps regions are very useful in detecting K57 and the new cps genotype.
Telomere-Associated Protein TIN2 Is Essential for Early Embryonic Development through a Telomerase-Independent Pathway (2004)

TIN2 is a negative regulator of telomere elongation that interacts with telomeric DNA repeat binding factor 1 (TRF1) and affects telomere length by a telomerase-dependent mechanism. Here we show that inactivation of the mouse TRF1-interacting protein 2 (TIN2) gene results in early embryonic lethality. We further observed that the embryonic lethality of TIN2 mutant mice was not affected by inactivation of the telomerase reverse transcriptase gene, indicating that embryonic lethality is not the result of telomerase-dependent changes in telomere length or function. Our findings suggest that TIN2 has a role independent of telomere length regulation that is essential for embryonic development and cell viability.
Wide-field imaging interferometry spatial-spectral image synthesis algorithms (2012)

The Wide-Field Imaging Interferometry Testbed (WIIT) is a wide-field spectral imaging Michelson interferometer developed at the NASA/Goddard Space Flight Center. WIIT is operational and effectively demonstrates imaging and spectroscopy over fields-of-view larger than the narrow primary beam footprint of a conventional Michelson interferometer. At the heart of this technique is the "double-Fourier" approach whereby the apertures and a delay line are both moved to collect interferograms over a 2D wide field detector grid simultaneously; one interferogram per detector pixel. This aggregate set of interferograms, as a function of baseline and delay line, is algorithmically processed to construct a single spatial-spectral cube with angular resolution approaching the ratio of the wavelength to the longest baseline. Herein we develop the mathematical spatial-spectral imaging model and the baseline processing algorithm and show results using simulated data and using WIIT testbed data.
A New Approach to Harness Data for Measuring Invisible Lost Time in Drilling Operations (2017)

Abstract Drilling operations can include invisible lost time (ILT), within productive time and nonproductive time (NPT). ILT is the time lost because a portion of the drilling operation is not performed at maximum efficiency. Current industry techniques use subjective decision making to calculate NPT, which only illustrates that ILT is present and does not address the root cause. By considering the dynamic downhole conditions and comparing the time necessary for various personnel to perform the same operations, a threshold time can be calculated for each operation, which is used to calculate NPT. After NPT is calculated, the real-time drilling data are converted to segmented drill-time data [i.e., the time necessary for each activity (Δt)] to convert to a time-series analysis problem. The algorithm developed decomposes the obtained time series into its intrinsic mode functions (IMFs) using the ensemble empirical mode decomposition (EMD), which tolerates residual noise in the signal. Mode mixing is a significant issue when the drilling data are converted into a time-series problem. Hence, an energy conservation principle is presented to identify and help eliminate the false mode components; thereby, only the components that truly represent the drilling activities are used for further calculations. The true characteristic IMFs are then combined with their weights to obtain a modified Δt series, which represents ILT. The weight estimation process is performed automatically to maximize the kurtosis and entropy of the Δt series. The NPT is calculated again from the modified Δt series using the technique previously described. The new NPT provides a higher value of NPT from which ILT can be computed using simple subtraction. After ILT is identified and calculated, the ILT cause can be ascertained by analyzing the drilling parameters, such as rate of penetration (ROP), weight on bit (WOB), torque, and flow rate, using an algorithm similar to the one previously discussed. The proposed method can be integrated with future management and well design plans to help improve drilling operation efficiency. The proposed workflow automates the entire calculation process, thereby reducing human interference and maximizing the time value of information. Additionally, this paper proposes another simpler analysis tool that is based on pattern analysis of the final IMF obtained from the decomposition of a time series. This observation-based tool proposes that if a process is nonproductive, then the final IMF will have a downward parabolic trend. If the personnel performance is consistent, then the final IMF will have an upward parabolic trend. This paper presents four field case studies to help prove the hypothesis of this work.
K-SVD dictionary-learning for the analysis sparse model (2012)

The synthesis-based sparse representation model for signals has drawn a considerable interest in the past decade. Such a model assumes that the signal of interest can be decomposed as a linear combination of a few atoms from a given dictionary. In this paper we concentrate on an alternative, analysis-based model, where an Analysis Dictionary multiplies the signal, leading to a sparse out-come. Our goal is to learn the analysis dictionary from a set of signal examples, and the approach taken is parallel and similar to the one adopted by the K-SVD algorithm that serves the corresponding problem in the synthesis model. We present the development of the algorithm steps, which include two greedy tailored pursuit algorithms and a penalty function for the dictionary update stage. We demonstrate its effectiveness in several experiments, showing a successful and meaningful recovery of the analysis dictionary.
Learning in the Frequency Domain (2020)

Deep neural networks have achieved remarkable success in computer vision tasks. Existing neural networks mainly operate in the spatial domain with fixed input sizes. For practical applications, images are usually large and have to be downsampled to the predetermined input size of neural networks. Even though the downsampling operations reduce computation and the required communication bandwidth, it removes both redundant and salient information obliviously, which results in accuracy degradation. Inspired by digital signal processing theories, we analyze the spectral bias from the frequency perspective and propose a learning-based frequency selection method to identify the trivial frequency components which can be removed without accuracy loss. The proposed method of learning in the frequency domain leverages identical structures of the well-known neural networks, such as ResNet-50, MobileNetV2, and Mask R-CNN, while accepting the frequency-domain information as the input. Experiment results show that learning in the frequency domain with static channel selection can achieve higher accuracy than the conventional spatial downsampling approach and meanwhile further reduce the input data size. Specifically for ImageNet classification with the same input size, the proposed method achieves 1.60% and 0.63% top-1 accuracy improvements on ResNet-50 and MobileNetV2, respectively. Even with half input size, the proposed method still improves the top-1 accuracy on ResNet-50 by 1.42%. In addition, we observe a 0.8% average precision improvement on Mask R-CNN for instance segmentation on the COCO dataset.
Purification and characterization of N-acetyl-D-hexosamine dehydrogenase from Pseudomonas sp. No. 53. (1989)

A new enzyme, N-acetyl-D-hexosamine dehydrogenase (N-acetyl-α-D-hexosamine:NAD+ 1-oxidoreductase), was purified to homogeneity on polyacrylamide gel electrophoresis from a strain of Pseudomonas sp. about 900-fold with a yield of 12%. The molecular weight of the enzyme was about 124, 000 on gel filtration and 30, 000 on SDS-polyacrylamide gel electrophoresis, respectively. Its isoelectric point was 4.7. The optimum pH was about 10.0. The enzyme was most stable between pH 8.0 and pH 10.5. The highest enzyme activity was observed with N-acetyl-D-glucosamine (Km=5.3mM) and N-acetyl-D-galactosamine (Km=0.8mM) as the sugar substrate. But it was not so active on N-acetyl-D-mannosamine. NAD+ was used specifically as the hydrogen acceptor. The anomeric requirement of the enzyme for N-acetyl-D-glucosamine was the α-pyranose form, and the reaction product was N-acetyl-D-glucosaminic acid. The enzyme activity was inhibited by Hg2+ and SDS, but many divalent cations, metal-chela ting reagents, and sulfhydryl reagents had no effect.
<title>Benefits of an image-oriented parallel file system</title> (1993)

Professionals in various fields such as medical imaging, biology, and civil engineering require rapid access to huge amounts of uncompressed pixmap image data. In order to fulfill these requirements, a parallel image server architecture is proposed, based on arrays of intelligent disk nodes, each disk node being composed of one processor and one disk. Pixmap image data is partitioned into rectangular extents, whose size and distribution among disk nodes minimize overall image access times. Disk node processors are responsible for maintaining both the data structure associated with their image file extents and an extent cache offering fast access to recently used data. Disk node processors may also be used for applying image processing operations to locally retrieved image parts. This contribution introduces the concept of an image oriented file system, where the file system is aware of image size, extent size, and extent distribution. Such an image oriented file system provides a natural way of combining parallel disk accesses and processing operations. The performance of the proposed multiprocessor-multidisk architecture is bounded either by communication throughput or by disk access speed. However, when disk accesses are combined with low-level local processing operations such as image size reduction (zooming), close to linear speedup factors can be obtained by increasing the number of intelligent disk nodes.
Strip- PET: a novel detector concept for the TOF-PET scanner (2012)

We briefly present a design of a new PET scanner based on strips of polymer scintillators arranged in a barrel constituting a large acceptance detector. The solution proposed is based on the superior timing properties of the polymer scintillators. The position and time of the reaction of the gamma quanta in the detector material will be determined based on the time of arrival of light signals to the edges of the scintillator strips.