gebhart/patrepeval huggingface dataset:
Virion Envelope Content, Infectivity, and Neutralization Sensitivity of Simian Immunodeficiency Virus (2005)

A truncating E767stop mutation was introduced into the envelope glycoprotein of simian immunodeficiency virus (SIV) strain SIV239-M5 (moderately sensitive to antibody-mediated neutralization and lacking five sites for N-linked carbohydrate attachment) and strain SIV316 (very sensitive to neutralization, with eight amino acid changes from the neutralization-resistant parental molecular clone, SIV239). The truncating mutation increased Env content in virions, increased infectivity, and decreased sensitivity to antibody-mediated neutralization in both strains. However, the magnitude of the effect on infectivity and neutralization sensitivity differed considerably between the two strains. In the context of strain SIV239-M5, truncation increased Env content in virions approximately 10-fold and infectivity in a reporter cell assay 24-fold. The truncated SIV239-M5 was only slightly more resistant to neutralization by polyclonal monkey sera and by monoclonal antibodies than SIV239-M5 with a full-length envelope glycoprotein. In the context of strain SIV316, truncation increased infectivity a dramatic 480-fold, while envelope content in virions was increased only about 14-fold. This dramatic increase in infectivity cannot be simply explained by the increase in envelope content and is likely due to an increase in inherent infectivity, i.e., infectivity per spike, that results from truncation. The truncated SIV316 was extremely resistant to antibody-mediated neutralization. In fact, it was not neutralized by any of the antibodies tested. When increasing amounts of SIV316 envelope glycoprotein (full length) were provided in trans to SIV316, infectivity was increased and sensitivity to neutralization was decreased, but to nowhere near the degree that was obtained when truncated SIV316 envelope glycoprotein was used. Truncated forms of SIV239 and SIV239-M5 required higher levels of soluble CD4 for inhibition of infection than their nontruncated forms; truncated SIV316 did not. Our results suggest that envelope content in SIV virions, infectivity, and resistance to antibody-mediated neutralization can be increased not only by truncation of the cytoplasmic domain but also by provision of excess envelope in trans. The striking increase in infectivity that results from truncation in the context of SIV316 appears to be due principally to an increase in inherent infectivity per spike.
Classification of Topologically Protected Gates for Local Stabilizer Codes (2013)

Given a quantum error correcting code, an important task is to find encoded operations that can be implemented efficiently and fault tolerantly. In this Letter we focus on topological stabilizer codes and encoded unitary gates that can be implemented by a constant-depth quantum circuit. Such gates have a certain degree of protection since propagation of errors in a constant-depth circuit is limited by a constant size light cone. For the 2D geometry we show that constant-depth circuits can only implement a finite group of encoded gates known as the Clifford group. This implies that topological protection must be "turned off" for at least some steps in the computation in order to achieve universality. For the 3D geometry we show that an encoded gate U is implementable by a constant-depth circuit only if UPU(†) is in the Clifford group for any Pauli operator P. This class of gates includes some non-Clifford gates such as the π/8 rotation. Our classification applies to any stabilizer code with geometrically local stabilizers and sufficiently large code distance.
Multi-Sensor Fusion in Automated Driving: A Survey (2019)

With the significant development of practicability in deep learning and the ultra-high-speed information transmission rate of 5G communication technology will overcome the barrier of data transmission on the Internet of Vehicles, automated driving is becoming a pivotal technology affecting the future industry. Sensors are the key to the perception of the outside world in the automated driving system and whose cooperation performance directly determines the safety of automated driving vehicles. In this survey, we mainly discuss the different strategies of multi-sensor fusion in automated driving in recent years. The performance of conventional sensors and the necessity of multi-sensor fusion are analyzed, including radar, LiDAR, camera, ultrasonic, GPS, IMU, and V2X. According to the differences in the latest studies, we divide the fusion strategies into four categories and point out some shortcomings. Sensor fusion is mainly applied for multi-target tracking and environment reconstruction. We discuss the method of establishing a motion model and data association in multi-target tracking. At the end of the paper, we analyzed the deficiencies in the current studies and put forward some suggestions for further improvement in the future. Through this investigation, we hope to analyze the current situation of multi-sensor fusion in the automated driving process and provide more efficient and reliable fusion strategies.
The System Iron–Titanium–Oxygen at 1200°C. and Oxygen Partial Pressures Between 1 Atm. and 2 × 10 <sup>−14</sup> Atm. (1961)

The 1200°C. isotherm in the system Fe‐Ti‐O has been studied by equilibrating mixtures of iron oxide (Fe 2 O 3 ) and titanium oxide (TiO 2 ) with atmospheres of controlled oxygen partial pressure. These atmospheresmnsisted of CO 2 , air, oxygen, mixtures of CO 2 and H 2 , and mixtures of CO 2 and CO. The resulting oxide mixtures were examined at room temperature by chemical analysis and by X‐ray diffraction. The stability regions of the α‐oxides (Fe m Ti 2‐m O 3 ), of the spinels, (Fe n Ti 3‐n O 4 ), and of the orthorhombic oxides (Fe p Ti 3‐p O 5 )were determined. Some nonstoichiometry occurs in the spinels and in the α‐oxides. The oxygen partial pressures at which spinel is reduced to (iron +α‐oxides) and at which α‐oxide (ilmenite) is reduced to (iron + orthorhombic oxide) were determined as 2.1 × 10 −13 and 9.3 × 10 −14 atm., respectively. The orthorhombic solid solution series extends over the whole range of oxygen partial pressures studied.
Interspecific comparison of a Drosophila gene encoding FMRFamide- related neuropeptides (1990)

In order to identify functionally important regions of a neuropeptide gene in Drosophila melanogaster, we have studied its occurrence in related species and have characterized the structure of a homologous gene in Drosophila virilis. The melanogaster gene encodes a precursor that contains 13 neuropeptides related to the molluscan tetrapeptide FMRFamide (Nambu et al., 1988; Schneider and Taghert, 1988). Using the melanogaster gene as a probe in Southern blot analysis, related sequences were detected in DNA from each of 7 species tested. D. virilis, which is estimated to have diverged from D. melanogaster between 60 and 80 million years ago (Throckmorton, 1975), was chosen for more detailed study. Immunocytochemical staining using an antibody to authentic FMRFamide revealed a similar set of immunoreactive neurons in the CNS of larvae from the 2 Drosophila species. Using a melanogaster gene probe, overlapping clones were isolated from a virilis genomic library; DNA sequence analysis indicated the presence of a homologous gene. Comparisons of the genes and deduced proteins between the 2 species revealed the following points. (1) Both genes are divided into 2 exons: in D. melanogaster the exons are 106 and 1352 bp long; in D. virilis, they are 169 and at least 1232 bp long; in both species, the intron is approximately 2.5 kb long. (2) The sequence of exon I has largely diverged, and in neither species are exon I sequences translated. In this vicinity of the gene, sequence conservation is limited to a 67 bp region that spans the TATA box and the RNA start site. (3) The deduced neuropeptide precursors have very similar sizes (347 vs 339 amino acids) and the presumed signal sequences are perfectly conserved. (4) While the melanogaster precursor contains 13 FMRFamide-related peptides, the virilis precursor contains only 10. (5) The sequences of some but not all of the FMRFamide-like peptides are perfectly conserved. (6) In the rest of the precursor, significant sequence conservation is found only in the N-terminal portion; immediately downstream of the final FMRFamide-like peptide, the protein sequences are highly divergent. (7) 5' to the RNA start sites (1.2 kb of melanogaster DNA and 1.8 kb of virilis DNA), 17 small (9-52 base pairs) regions are evolutionarily conserved (greater than 80% sequence conservation). We discuss neuropeptide biosynthesis, the functions and evolution of FMRFamide-like neuropeptides in insects, and the cell-specific regulation of neuropeptide gene expression in the contexts of these results.
Bacterial Predators of <i>Micrococcus luteus</i> in Soil (1980)

Micrococcus luteus cells died relatively rapidly when they were added to natural soil. Microscopic observation showed that the cells were being physically destroyed by bacterial predators in the soil. Two of these predators were responsible for the initial, main attack, and they were isolated. The isolates on laboratory media lysed M. luteus cells in a manner similar to the attacks that occurred in soil. Neither predator was obligate, however, nor were they nutritionally fastidious. One of these bacteria produced mycelium and conidia. Under nutritionally poor conditions it used slender filaments of mycelium to seek out host cells. It had at least some of the characteristics of a Streptoverticillium species. The other bacterium was a short, gram-negative rod that did not easily fit into any of the known groups of gram-negative bacteria. It attached to host cells, but its mechanism of lysing these cells is not known.
Properties of purified gut trypsin from <i>Helicoverpa zea</i>, adapted to proteinase inhibitors (2002)

Pest insects such as Helicoverpa spp. frequently feed on plants expressing protease inhibitors. Apparently, their digestive system can adapt to the presence of protease inhibitors. To study this, a trypsin enzyme was purified from the gut of insects that were raised on an inhibitor-containing diet. The amino-acid sequence of this enzyme was analysed by tandem MS, which allowed assignment of 66% of the mature protein amino acid sequence. This trypsin, called HzTrypsin-S, corresponded to a known cDNA sequence from Helicoverpa. The amino acid sequence is closely related (76% identical) to that of a trypsin, HzTrypsin-C, which was purified and identified in a similar way from insects raised on a diet without additional inhibitor. The digestive properties of HzTrypsin-S and HzTrypsin-C were compared. Both trypsins appeared to be equally efficient in degrading protein. Four typical plant inhibitors were tested in enzymatic measurements. HzTrypsin-S could not be inhibited by > 1000-fold molar excess of any of these. The same inhibitors inhibited HzTrypsin-C with apparent equilibrium dissociation constants ranging from 1 nm to 30 nm. Thus, HzTrypsin-S seems to allow the insect to overcome different defensive proteinase inhibitors in plants.
Characterization of the signaling function of MHC class II molecules during antigen presentation by B cells (1991)

In addition to their role as peptide binding proteins, MHC class II proteins can also function as signal transducing molecules. Recent work using B cells expressing genetically engineered truncated MHC class II molecules has suggested that signaling through the cytoplasmic domains of these proteins plays an important role in the generation of signals required for the activation of some T cell hybrids. Treatment of truncated Ia-expressing B cells with cAMP-elevating agents corrects the deficiency in Ag presentation by these cells. We report that the MHC class II-mediated signal appears to act by a mechanism that increases the efficiency of Ag presentation by B cells thereby lowering the amount of specific Ag required for T cell activation. We further show that the induction of the cAMP-induced signal in B cells is inhibited by cycloheximide and cytochalasin A, implicating protein synthesis as well as cytoskeletal rearrangements in Ag presentation to accessory signal- dependent hybrids. In contrast, these agents do not block Ag presentation to a T cell hybrid previously shown not to require the cAMP-induced signal for activation. The signal-dependent T hybrid is additionally dependent on LFA-1-ICAM-1 interaction for activation, whereas the signal-independent hybrid is not. These observations suggest the existence of two types of T cell hybrid with respect to their requirements for activation: those that require only the recognition of MHC class II-peptide complexes without accessory signals, as shown by their ability to respond to purified Ia on planar membranes, and those that, in addition to recognition of MHC II/Ag, require LFA-1-ICAM-1 interaction and the delivery of additional signal(s) induced in the B cell via signal transduction through MHC class II molecules.
Reversible folding of rhodanese (1989)

For the first time completely reversible unfolding was achieved for guanidinium chloride-denatured rhodanese using a systematically defined protocol. These conditions included beta-mercaptoethanol, lauryl maltoside, and sodium thiosulfate. All components were required to get more than the previous best reactivation with lauryl maltoside of 17% (Tandon, S., and Horowitz, P. (1986) J. Biol. Chem. 261, 15615-15681). Non-coincidental transition curves were obtained by monitoring different parameters including: (i) variation in the activity, (ii) shifts of the fluorescence wavelength maximum, and (iii) variation in ellipticity at 220 nm. The transition followed by the fluorescence wavelength maximum was asymmetric and resolvable into two separate transitions. A thermodynamic analysis was used to define the energetics of the two processes. Studies with the fluorescent "apolar" probe 1,8ANS are consistent with the appearance of organized hydrophobic surfaces following the first transition. Near UV CD measurements indicated that the first transition is associated with a loss of dyssymmetry around at least some of the tryptophans. Thus, the unfolding of rhodanese is complex, and there are detectable intermediate(s) during the process. These results suggest that reversible unfolding occurs in two discrete stages: 1) loss of tertiary interactions and activity, with retention of secondary structure, and 2) loss of secondary structure. The available x-ray structure suggests that the first transition can be associated with changes in the domain interactions, which may modulate the effectiveness of helix dipoles in lowering the pKa of the active site sulfhydryl.
Time-Intensity Curves Obtained after Microbubble Injection Can Be Used to Differentiate Responders from Nonresponders among Patients with Clinically Active Crohn Disease after 6 Weeks of Pharmacologic Treatment (2016)

Purpose To assess whether contrast material-enhanced ultrasonography (US) can be used to differentiate responders from nonresponders among patients with clinically active Crohn disease after 6 weeks of pharmacologic treatment. Materials and Methods This prospective study was approved by our ethics committee, and written informed consent was obtained from all patients. Fifty consecutive patients (26 men and 24 women; mean age, 34.76 years ± 9) with a proved diagnosis of active Crohn disease who were scheduled to begin therapy with biologics (infliximab or adalimumab) were included, with enrollment from June 1, 2013, to June 1, 2015. In each patient, the terminal ileal loop was imaged with contrast-enhanced US before the beginning and at the end of week 6 of pharmacologic treatment. Time-intensity curves obtained in responders (those with a decrease in the Crohn disease endoscopic index of severity score of 25-44 before treatment to 10-15 after treatment, an inflammatory score <7, and/or a decrease ≥70 in the Crohn disease activity index score compared with baseline) and nonresponders were compared with Mann-Whitney test. Results Responders (n = 31) and nonresponders (n = 19) differed (P < .05) in the percent change of peak enhancement (-40.78 ± 62.85 vs 53.21 ± 72.5; P = .0001), wash-in (-34.8 ± 67.72 vs 89.44 ± 145.32; P = .001) and washout (-5.64 ± 130.71 vs 166.83 ± 204.44; P = .002) rate, wash-in perfusion index (-42.29 ± 59.21 vs 50.96 ± 71.13; P = .001), area under the time-intensity curve (AUC; -46.17 ± 48.42 vs 41.78 ± 87.64; P = .001), AUC during wash-in (-43.93 ± 54.29 vs 39.79 ± 70.85; P = .001), and AUC during washout (-49.36 ± 47.42 vs 42.65 ± 97.09; P = .001). Responders and nonresponders did not differ in the percent change of rise time (5.09 ± 49.13 vs 6.24 ± 48.06; P = .93) and time to peak enhancement (8.82 ± 54.5 vs 10.21 ± 43.25; P = .3). Conclusion Analysis of time-intensity curves obtained after injection of microbubble contrast material 6 weeks after beginning pharmacologic treatment can be used to differentiate responders from nonresponders among patients with clinically active Crohn disease. <sup>©</sup> RSNA, 2016.
Interleukin-17A-Induced Human Mesenchymal Stem Cells Are Superior Modulators of Immunological Function (2015)

Interferon-γ (IFN-γ)-preactivated mesenchymal stem cells (MSC-γ) are highly immunosuppressive but immunogenic in vivo due to their inherent expression of major histocompatibility (MHC) molecules. Here, we present an improved approach where we modified human bone marrow-derived MSC with interleukin-17A (MSC-17) to enhance T cell immunosuppression but not their immunogenicity. MSC-17, unlike MSC-γ, showed no induction or upregulation of MHC class I, MHC class II, and T cell costimulatory molecule CD40, but maintained normal MSC morphology and phenotypic marker expression. When cocultured with phytohemagglutinin (PHA)-activated human T cells, MSCs-17 were potent suppressors of T cell proliferation. Furthermore, MSC-17 inhibited surface CD25 expression and suppressed the elaboration of Th1 cytokines, IFN-γ, tumor necrosis factor-α (TNF-α), and IL-2 when compared with untreated MSCs (UT-MSCs). T cell suppression by MSC-17 correlated with increased IL-6 but not with indoleamine 2,3-dioxygenase 1, cyclooxygenase 1, and transforming growth factor β-1. MSC-17 but not MSC-γ consistently induced CD4(+) CD25(high) CD127(low) FoxP3(+) regulatory T cells (iTregs) from PHA-activated CD4(+) CD25(-) T cells. MSC-induced iTregs expressed CD39, CD73, CD69, OX40, cytotoxic T-lymphocyte associated antigen-4 (CTLA-4), and glucocorticoid-induced TNFR-related protein (GITR). These suppressive MSCs-17 can engender Tregs to potently suppress T cell activation with minimal immunogenicity and thus represent a superior T cell immunomodulator for clinical application.
Retinoid X Receptor Is a Nonsilent Major Contributor to Vitamin D Receptor-Mediated Transcriptional Activation (2003)

The vitamin D receptor (VDR) belongs to the thyroid hormone/retinoid receptor subfamily of nuclear receptors and functions as a heterodimer with retinoid X receptor (RXR). The RXR-VDR heterodimer, in contrast to other members of the class II nuclear receptor subfamily, is nonpermissive where RXR does not bind its cognate ligand, and therefore its role in VDR-mediated transactivation by liganded RXR-VDR has not been fully characterized. Here, we show a unique facet of the intermolecular RXR-VDR interaction, in which RXR actively participates in vitamin D3-dependent gene transcription. Using helix 3 and helix 12 mutants of VDR and RXR, we provide functional evidence that liganded VDR allosterically modifies RXR from an apo (unliganded)- to a holo (liganded)-receptor conformation, in the absence of RXR ligand. As a result of the proposed allosteric modification of RXR by liganded VDR, the heterodimerized RXR shows the "phantom ligand effect" and thus acquires the capability to recruit coactivators steroid receptor coactivator 1, transcriptional intermediary factor 2, and amplified in breast cancer-1. Finally, using a biochemical approach with purified proteins, we show that RXR augments the 1,25-dihydroxyvitamin D3-dependent recruitment of transcriptional intermediary factor 2 in the context of RXR-VDR heterodimer. These results confirm and extend the previous observations suggesting that RXR is a significant contributor to VDR-mediated gene expression and provide a mechanism by which RXR acts as a major contributor to vitamin D3-dependent transcription.
Determination of surface nanostructure from analysis of electron plasmon losses in XPS (2002)

Abstract We have explored the possibility of obtaining information about the surface nanostructure (i.e., how a given phase of material is distributed near to the surface region) from the analysis of loss plasmons that appear in the lower kinetic energy side of photoelectron and Auger peaks. First, we show an example where information is mainly obtained from the position of the plasmon peak. In practice, two‐dimensional growth of an Al 2 O 3 deposit on SiO 2 is deduced by identification of surface plasmon excitation due to electron transport of the corresponding Al KLL signal. Furthermore, a new method based on a quantitative (plasmon peak intensity) description of the single plasmon excitation that appears behind a photoelectron peak is proposed. This method has been applied to describe the growth mechanism of MgO deposited by evaporation on TiO 2 . Thus, it is shown that MgO grows with strong island formation according to the analysis. The consistency of the proposed method is supported by factor analysis of the loss structure behind the Mg 1s peak. Moreover, the validity of the proposed method has been checked using Tougaard background analysis for the same system. From these results, an alternative method, based on analysis of the plasmon structure observed behind x‐ray photoelectron peaks, is proposed for characterization of the nanostructure in this type of system. Copyright © 2002 John Wiley & Sons, Ltd.
The purification and characterization of a β-glucosidase from <i>Alcaligenes faecalis</i> (1986)

The beta-glucosidase from Alcaligenes faecalis has been purified to homogeneity (880-fold purification, 11% yield) using a combination of classical techniques and medium pressure ion-exchange chromatography. It is a dimeric enzyme of monomer molecular weight 50,000 and has no specific requirement for divalent metal ions. It has a high specificity for beta-glucosides and hydrolyses a wide variety of different chemical types wit retention of configuration at the anomeric centre. It has no exo-beta-1,4-glucanase activity. It is reversibly inhibited by a variety of sugars which have been shown previously to be very active against glucosidases, suggesting a normal mechanism of action. Measured Km values for cellobiose and p-nitrophenyl beta-D-glucopyranoside are quite low (0.70 and 0.08 mM, respectively), making this a good choice for cocloning into a cellulase system optimized for glucose production.