gebhart/patrepeval huggingface dataset:
Defective cation-coupling mutants of Escherichia coli Na+/proline symport carrier. Characterization and localization of mutations. (1990)

A major proline carrier in Escherichia coli encoded by the putP gene mediates proline/Na+ or Li+ symport. Proline carrier mutants with altered cation specificity were obtained by mutagenesis with nitrous acid in vitro of a plasmid carrying the wild-type putP gene. Two mutant strains harboring plasmid pMOP4135 and pMOP4141 could transport proline efficiently only in the presence of an increased concentration of sodium ion. Mutations of these plasmids, putP4135 and putP4141, caused reduction of affinity for Na+ of proline transport and binding, without remarkable change in the affinity for proline or in production of the carriers. Consistent with the lower affinity of the putP4141 carrier for Na+, the mutant carrier was supersensitive to N-ethylmaleimide inhibition. The pH dependence of proline binding was also changed in these mutant carriers. The lesions of putP4135 and putP4141 were located in the N-terminal part of the putP gene (ClaI-PvuII fragment) by in vitro recombination and subsequent examination of the phenotype of the transformants. DNA sequencing of these fragments revealed one base alteration of G to A at nucleotides 299 and 656 in pMOP4141 and pMOP4135, respectively, which corresponded to amino acid changes from Gly22 to glutamic acid and Cys141 to tyrosine, respectively.
A Transgenic-Mouse Model of Amyotrophic Lateral Sclerosis (1994)

Few diseases are as debilitating and inevitably lethal as amyotrophic lateral sclerosis (ALS). The disease typically strikes adults in midlife, causing paralysis and death within five years. The cause of most cases remains unknown, and the disease is untreatable. About 10 percent of patients have an inherited form of the disease. In 1993 a multicenter study reported that some cases of familial ALS arise because of mutations in the gene encoding the cytosolic form of the enzyme copper-zinc superoxide dismutase (SOD1).1 This enzyme detoxifies the superoxide anion, a ubiquitous byproduct of aerobic metabolism. As a free radical (free to diffuse . . .
Distinct changes in the laminin composition of basement membranes in human seminiferous tubules during development and degeneration. (1997)

We studied the distribution of laminin (Ln) chains and their integrin (Int) receptors in normal developing and adult and in atrophied human testes by using immunohistochemistry. Immunostaining for EHS Ln and type IV collagen was used to identify basement membranes (BMs). In the BM of seminiferous epithelium of fetal testis, a panel of monoclonal antibodies showed immunoreactivity for Ln alpha 1-, alpha 2-, beta 1-, beta 2- and gamma 1-chains, suggestive of the presence of Lns 1 to 3. In BM of adult seminiferous epithelium with active spermatogenesis, immunoreactivity for Ln beta 2- and gamma 1-chains was found but not for Ln alpha-chains, suggesting a complex of Ln chains not compatible with any known trimers. Instead, with polyclonal Ln antiserum and monoclonal antibody to type IV collagen, a distinct BM-like reactivity was seen. In atrophied testes, prominent immunoreactivities for Ln chains, compatible with Lns 1 to 3, were seen in the thickened BM of seminiferous tubules, hence suggestive of reappearance of fetal Lns. Among the subunits of Ln-binding Int receptors in fetal seminiferous tubules, a strong immunoreactivity for Int beta 1- and Int alpha 6-subunits was seen throughout the seminiferous epithelium, other Int subunits being found in interstitial cells. In the adult and atrophied testes, immunoreactivities for Int beta 1- and Int alpha 6-subunits were seen to be confined to the basal aspect of the seminiferous epithelium whereas immunoreactivities for Int alpha 1-, alpha 2-, alpha 3- and beta 4-subunits were seen in the myoid cells. The results show that both maturation and degenerative changes of human testes are accompanied by distinct changes in the Ln expression of BM of seminiferous epithelium, which appears to accompany epithelial differentiation of the Sertoli cells. Furthermore, they suggest the presence of a novel Ln trimer in BM of adult human seminiferous tubules.
Effect of intravenous amino acids on glutamine and protein kinetics in low-birth-weight preterm infants during the immediate neonatal period (2005)

Glutamine may be a conditionally essential amino acid in low-birth-weight (LBW) preterm neonates. Exogenously administered amino acids, by providing anaplerotic carbon into the tricarboxylic acid cycle, could result in greater cataplerotic efflux and glutamine de novo synthesis. The effect of dose and duration of amino acid infusion on glutamine and nitrogen (N) kinetics was examined in LBW infants in the period immediately after birth. Preterm neonates (<32 weeks gestation, birth weights 809-1,755 g) were randomized to initially receive either 480 or 960 micromol x kg(-1) x h(-1) of an intravenous amino acid solution for 19-24 hours, followed by a higher or lower amino acid load for either 5 h or 24 h. Glutamine de novo synthesis, leucine N, phenylalanine, and urea kinetics were determined using stable isotopic tracers. An increase in amino acid infusion from 480 to 960 micromol x kg(-1) x h(-1) for 5 h resulted in decreased glutamine de novo synthesis in every neonate (384.4 +/- 38.0 to 368.9 +/- 38.2 micromol x kg(-1) x h(-1), P < 0.01) and a lower whole body rate of proteolysis (P < 0.001) and urea synthesis (P < 0.001). However, when the increased amino acid infusion was extended for 24 h, glutamine de novo synthesis increased (369.7 +/- 92.6 to 483.4 +/- 97.5 micromol x kg(-1) x h(-1), P < 0.001), whole body rate of proteolysis did not change, and urea production increased. Decreasing the amino acid load resulted in a decrease in glutamine rate of appearance (R(a)) and leucine N R(a), but had no effect on phenylalanine R(a). Acutely stressed LBW infants responded to an increase in amino acid load by transiently suppressing whole body rate of glutamine synthesis, proteolysis, and oxidation of protein. The mechanisms of this transient effect on whole body protein/nitrogen metabolism remain unknown.
Assessment of pupil size under different light intensities using the Procyon pupillometer (2006)

The linear relationship between the pupil size and the log unit of the light intensity showed a tight correlation in all cases. These results can be useful in the comparing pupil size with pupillometers that work under different light conditions.
Motion Fused Frames: Data Level Fusion Strategy for Hand Gesture Recognition (2018)

Acquiring spatio-temporal states of an action is the most crucial step for action classification. In this paper, we propose a data level fusion strategy, Motion Fused Frames (MFFs), designed to fuse motion information into static images as better representatives of spatio-temporal states of an action. MFFs can be used as input to any deep learning architecture with very little modification on the network. We evaluate MFFs on hand gesture recognition tasks using three video datasets - Jester, ChaLearn LAP IsoGD and NVIDIA Dynamic Hand Gesture Datasets - which require capturing long-term temporal relations of hand movements. Our approach obtains very competitive performance on Jester and ChaLearn benchmarks with the classification accuracies of 96.28% and 57.4%, respectively, while achieving state-of-the-art performance with 84.7% accuracy on NVIDIA benchmark.
Structural elucidation of 11-hydroxy-12,13-epoxyoctadeca-(9Z, 15Z)-dienoic acids from rice plants suffering from rice blast disease (1986)

T. Kato, Y. Yamaguchi, S. Ohnuma, T. Uyehara, T. Namai, M. Kodama and Y. Shiobara, J. Chem. Soc., Chem. Commun., 1986, 743b DOI: 10.1039/C3986000743B
A Somatic Variant in MYD88 (L265P) Revealed by Whole Genome Sequencing Differentiates Lymphoplasmacytic Lymphoma From Marginal Zone Lymphomas (2011)

Abstract Abstract 261 Lymphoplasmacytic (LPL) and marginal zone lymphoma (MZL) are distinct clinicopathological entities under the WHO classification system for B-cell lymphomas. Differentiation of LPL from MZL has been difficult due to overlapping clinical, morphological, histopathological, immunophenotypic, and cytogenetic features. We therefore sought to identify a molecular marker by which LPL could be differentiated from MZL. Using paired normal/tumor tissues from 10 LPL patients, whole genome sequencing was utilized to identify somatic variants. These studies identified a somatic variant at position 38182641 in chromosome 3p22.2 with a single nucleotide change from T→C in the myeloid differentiation primary response (MYD88) gene, and a predicted non-synonymous change at amino acid position 265 from leucine to proline (L265P) in 10 of 10 LPL patients. MYD88 L265P is an oncogenically active mutation in DLBCL ABC cell lines via activation of IRAK1/4/TRAF-6/NF-κβ signaling, and is present in tumors from 29% of patients with ABC subtype of DLBCL, and 6% of patients with MALT lymphomas (Ngo et al, Nature 2011, 470:115–119). Further to these efforts, we performed Sanger sequencing of MYD88 in malignant cells obtained from 51 patients with LPL, 49 of whom had an IgM monoclonal protein and were therefore classified as Waldenstrom's Macroglobulinemia (WM), and 2 with an IgG monoclonal protein, along with 46 patients with MZL, which included 21 Splenic (SMZL), 20 Extranodal (EMZL), and 5 Nodal (NMZL) Subtypes, as well as B-cells from 15 healthy donors. Among LPL patients, the MYD88 L265P variant was found in malignant cells from 46/51 (90.1%) cases, which included 44 patients with WM, and 2 patients with IgG LPL. Expression of the MYD88 L265P variant was heterozygous in 42, and homozygous in 4 LPL patients. By comparison, only 3/46 (6.5%) patients with MZL (1 SMZL; 1 EMZL; 1 NMZL) exhibited the MYD88 L265P variant which was heterozygous (p<0.0001), and included 2 patients (1 SMZL, 1 NMZL) with extensive bone marrow involvement, a monoclonal IgM protein, and whose clinicopathological characteristics overlapped with LPL. By comparison, the MYD88 L265P variant was absent in CD19+ cells from all 15 healthy donors. The results of this study demonstrate that the MYD88 L265P mutation is widely expressed in patients with LPL, and can be used to differentiate LPL from MZL. Disclosures: Treon: Millennium: Consultancy, Membership on an entity's Board of Directors or advisory committees; Celgene: Membership on an entity's Board of Directors or advisory committees.
A portable virtual machine for program debugging and directing (2004)

Directors are reactive systems that monitor the run-time environment and react to the emitted events. Typical examples of directors are debuggers and tools for program analysis and software visualization. In this paper we describe a cross-platform virtual machine that provides advanced facilities for implementing directors with low effort.
Robust real-time tracking on an active vision head (2002)

Achieving the first step of a framework for human-robot interaction, we have designed a binocular tracking system which uses disparity and velocity information for the detection and pursuit of moving objects in cluttered environments without a-priori knowledge of the target shape or texture. The implemented system robustly tracks in real-time deformable objects such as human hands and faces, taking advantage of the mechanical and optical properties of ESCHeR, a high performances active vision head equipped with foveated wide-angle lenses.
Small Molecule Probe Suitable for <i>In Situ</i> Profiling and Inhibition of Protein Disulfide Isomerase (2013)

Proper folding of cellular proteins is assisted by protein disulfide isomerases (PDIs) in the endoplasmic reticulum of mammalian cells. Of the at least 21 PDI family members known in humans, the 57-kDa PDI has been found to be a potential therapeutic target for a variety of human diseases including cancer and neurodegenerative diseases. Consequently, small molecule PDI-targeting inhibitors have been actively pursued in recent years, and thus far, compounds possessing moderate inhibitory activities (IC50 between 0.1 and 100 μM against recombinant PDI) have been discovered. In this article, by using in situ proteome profiling experiments in combination with in vitro PDI enzymatic inhibition assays, we have discovered a phenyl vinyl sulfonate-containing small molecule (P1; shown) as a relatively potent and specific inhibitor of endogenous human PDI in several mammalian cancer cells (e.g., GI50 ∼ 4 μM). It also possesses an IC50 value of 1.7 ± 0.4 μM in an in vitro insulin aggregation assay. Our results indicate P1 is indeed a novel, cell-permeable small molecule PDI inhibitor, and the electrophilic vinyl sulfonate scaffold might serve as a starting point for future development of next-generation PDI inhibitors and probes.
Digital Autofocus Using Scene Content (1985)

A real-time digital scene based focusing algorithm, which will be implemented on the Honeywell FUR is described. Focus merit functions (FMF) which are optimal for Honeywell FUR imagery are examined. The algorithm was tested by demonstrating its capability to focus on a static scene.
Automatic translation of software binaries onto FPGAs (2004)

The introduction of advanced FPGA architectures, with built-in DSP support, has given DSP designers a new hardware alternative. By exploiting its inherent parallelism, it is expected that FPGAs can outperform DSP processors. This paper describes the process and considerations for automatically translating binaries targeted for general DSP processors into Register Transfer Level (RTL) VHDL or Verilog code to be mapped onto commercial FPGAs. The Texas Instruments C6000 DSP processor architecture is chosen as the DSP processor platform, and the Xilinx Virtex II as a target FPGA. Various optimizations are discussed, including data dependency analysis, procedure extraction, induction variable analysis, memory optimizations, and scheduling. Experimental results on resource usage and performance are shown for ten software binary benchmarks. Results show performance gains of 3-20X in the FPGA designs over that of the DSP processors in terms of reductions of execution cycles.
Role of certain trace minerals in oxidative stress, inflammation, CD4/CD8 lymphocyte ratios and lung function in asthmatic patients (2011)

Abnormal distributions of these trace minerals may aggravate oxidative damage and inflammation, increased CD4/CD8 lymphocyte ratios and decreased lung function in asthma.
Magnetic propulsion along an orbiting grain stream (1986)

Covers advancements in spacecraft and tactical and strategic missile systems, including subsystem design and application, mission design and analysis, materials and structures, developments in space sciences, space processing and manufacturing, space operations, and applications of space technologies to other fields.
Mesolimbic Dopamine Neurons in the Brain Reward Circuit Mediate Susceptibility to Social Defeat and Antidepressant Action (2010)

We previously reported that the activity of mesolimbic dopamine neurons of the ventral tegmental area (VTA) is a key determinant of behavioral susceptibility vs resilience to chronic social defeat stress. However, this was based solely on ex vivo measurements, and the in vivo firing properties of VTA dopamine neurons in susceptible and resilient mice, as well as the effects of antidepressant treatments, remain completely unknown. Here, we show that chronic (10 d) social defeat stress significantly increased the in vivo spontaneous firing rates and bursting events in susceptible mice but not in the resilient subgroup. Both the firing rates and bursting events were significantly negatively correlated with social avoidance behavior, a key behavioral abnormality induced by chronic social defeat stress. Moreover, the increased firing rates, bursting events, and avoidance behavior in susceptible mice were completely reversed by chronic (2 week), but not acute (single dose), treatments with the antidepressant medication fluoxetine (20 mg/kg). Chronic social defeat stress increased hyperpolarization-activated cation current (I(h)) in VTA dopamine neurons, an effect that was also normalized by chronic treatment with fluoxetine. As well, local infusion of I(h) inhibitors ZD7288 (0.1 μg) or DK-AH 269 (0.6 μg) into the VTA exerted antidepressant-like behavioral effects. Together, these data suggest that the firing patterns of mesolimbic dopamine neurons in vivo mediate an individual's responses to chronic stress and antidepressant action.
Revisiting the Open-Domain Question Answering Pipeline (2020)

Open-domain question answering (QA) is the tasl of identifying answers to natural questions from a large corpus of documents. The typical open-domain QA system starts with information retrieval to select a subset of documents from the corpus, which are then processed by a machine reader to select the answer spans. This paper describes Mindstone, an open-domain QA system that consists of a new multi-stage pipeline that employs a traditional BM25-based information retriever, RM3-based neural relevance feedback, neural ranker, and a machine reading comprehension stage. This paper establishes a new baseline for end-to-end performance on question answering for Wikipedia/SQuAD dataset (EM=58.1, F1=65.8), with substantial gains over the previous state of the art (Yang et al., 2019b). We also show how the new pipeline enables the use of low-resolution labels, and can be easily tuned to meet various timing requirements.
Role of Tumor Necrosis Factor Alpha, Interleukin-1β, and Interleukin-6 in a Mouse Model of Group B Streptococcal Arthritis (1999)

Intravenous inoculation of CD1 mice with 10(7) CFU of type IV group B Streptococcus (GBS IV) results in a high incidence of diffuse septic arthritis. In this study the roles of tumor necrosis factor alpha (TNF-alpha), interleukin-1beta (IL-1beta), and IL-6 in articular pathology were evaluated. Cytokine levels were quantified in the serum and joints by enzyme-linked immunosorbent assay in mice injected with GBS IV and tested or not tested with pentoxifylline (PTF), a methylxanthine that affects cytokine production. PTF was administered intraperitoneally at a dose of 1 mg/mouse (50 mg/kg of body weight) 1 h after GBS infection and then at 24-h intervals for 4 days. High levels of IL-1beta and IL-6, but not TNF-alpha, were detected in the joints of mice injected with GBS IV from 5 to 15 days after infection, when articular lesions were most frequent and severe. IL-1beta and IL-6 concentrations in the joints significantly (P < 0.001) exceeded those detected in the serum, confirming a strong local production. PTF treatment resulted in a strong reduction of cytokine production and in a marked decrease in both the incidence and severity of arthritis. Inoculation of exogenous murine recombinant IL-1beta or IL-6 in mice treated with GBS IV plus PTF resulted in an incidence and severity of articular lesions similar to those obtained with inoculation of GBS IV alone. No significant effect was obtained with TNF-alpha administration. These data show a strong involvement of IL-1beta and IL-6, but not TNF-alpha, in the pathogenesis of GBS arthritis.
Mobile Optimized Digital Identity (MODI): A framework for easier digital certificate use (2013)

Traditional authentication methods such as passwords no longer meet all the security requirements of today's enterprise. Digital certificates provide a much more secure, resilient alternative solution. However, digital certificates are cumbersome to use for an end-user and are complex to implement for a resource provider. In this paper, we describe the Mobile Optimized Digital Identity (MODI) framework, which aims to solve the logistical issues of using certificates as an authentication method for both the end-user and the resource provider. The MODI framework consists of three tightly integrated components that work in concert: a mobile device application (MDA), an authentication toolkit, and a trusted third-party the security broker (SB). With a dedicated MODI MDA, certificate deployment, maintenance, and use are greatly simplified for the end-user. The MODI authentication toolkit enables resource providers to easily integrate with the framework, thus shielding developers from needing any knowledge of digital certificates and their implementation. Using mobile devices, the end-user authentication tool allows the MODI solution to expand its scope beyond conventional network access to novel physical access scenarios with the aid of proximity scanning technologies such as near-field communication (NFC).
Sensitivity of a fiber-optic gyroscope to environmental magnetic fields (1982)

It is shown that environmental magnetic fields may cause a considerable error for the detected rotation rate even though the line integral of the magnetic field along the fiber vanishes. Experimentally, it has been shown that the earth's magnetic field yields a bias uncertainty of about 10 degrees /h, which can be reduced by at least 1 order of magnitude if the fiber coil is protected against environmental magnetic fields.
[60]Fullerene-Fused Lactones:  Manganese(III) Acetate-Mediated Synthesis and Novel Reductive Ring Opening (2006)

[reaction: see text] [60]Fullerene-fused lactones were prepared by the manganese(III) acetate-mediated reactions of [60]fullerene with carboxylic acids, carboxylic anhydrides, or malonic acids. Novel reductive ring opening of the lactones with Grignard reagents was observed.
REAL: A retention error aware LDPC decoding scheme to improve NAND flash read performance (2016)

Continuous technology scaling makes NAND flash cells much denser. As a result, NAND flash is becoming more prone to various interference errors. Due to the hardware circuit design mechanisms of NAND flash, retention errors have been recognized as the most dominant errors, which affect the data reliability and flash lifetime. Furthermore, after experiencing a large number of programm/erase (P/E) cycles, flash memory would suffer a much higher error rate, rendering traditional ECC codes (typically BCH codes) insufficient to ensure data reliability. Therefore, low density parity check (LDPC) codes with stronger error correction capability are used in NAND flash-based storage devices. However, directly using LDPC codes with belief propagation (BP) decoding algorithm introduces non-trivial overhead of decoding latency and hence significantly degrades the read performance of NAND flash. It has been observed that flash retention errors show the so-called numerical-correlation characteristic (i.e., the 0-1 bits stored in the flash cell affect each other with the leakage of the charge) in each flash cell. In this paper, motivated by the observed characteristic, we propose REAL: a retention error aware LDPC decoding scheme to improve NAND flash read performance. The developed REAL scheme incorporates the numerical-correlation characteristic of retention errors into the process of LDPC decoding, and leverages the characteristic as additional bits decision information to improve its error correction capabilities and decrease the decoding latency. Our simulation results show that the proposed REAL scheme can reduce the LDPC decoding latency by 26.44% and 33.05%, compared with the Logarithm Domain Min-Sum (LD-MS) and Probability Domain BP (PD-BP) schemes, respectively.
Superresolved imaging based on wavelength multiplexing of projected unknown speckle patterns (2015)

We propose a method for resolution enhancement of a diffraction limited optical system based on the capture of a set of low resolution images. These images are obtained after projection of an ensemble of unknown speckle patterns on top of the high resolution object that is to be imaged. Each speckle pattern is generated by the same thin (and unknown) diffuser, but illuminated with a slightly different wavelength. From the ensemble of low resolution images, we obtain a system of equations that can be solved in an iterative manner that enables reconstruction of the high resolution object. As a result, we also achieve the projected high resolution speckle patterns used for the encoding.