gebhart/patrepeval huggingface dataset:
Properties of lysophosphatidylcholine acyltransferase from Brassica napus cultures (2003)

Acyl-CoA:lysophosphatidylcholine acyltransferase (LPCAT; EC 2.3.1.23) catalyzes the acyl-CoA-dependent acylation of lysophosphatidylcholine (LPC) to produce PC and CoA. LPCAT activity may affect the incorporation of fatty acyl moieties at the sn-2 position of PC where PUFA are formed and may indirectly influence seed TAG composition. LPCAT activity in microsomes prepared from microspore-derived cell suspension cultures of oilseed rape (Brassica napus L. cv Jet Neuf) was assayed using [1-14C]acyl-CoA as the fatty acyl donor. LPCAT activity was optimal at neutral pH and 35 degrees C, and was inhibited by 50% at a BSA concentration of 3 mg mL(-1). At acyl-CoA concentrations above 20 microM, LPCAT activity was more specific for oleoyl (18:1)-CoA than stearoyl (18:0)- and palmitoyl (16:0)-CoA. Lauroyl (12:0)-CoA, however, was not an effective acyl donor. LPC species containing 12:0, 16:0, 18:0, or 18:1 as the fatty acyl moiety all served as effective acyl acceptors for LPCAT, although 12:0-LPC was somewhat less effective as a substrate at lower concentrations. The failure of LPCAT to catalyze the incorporation of a 12:0 moiety from acyl-CoA into PC is consistent with the tendency of acyltransferases to discriminate against incorporation of this fatty acyl moiety at the sn-2 position of TAG from the seed oil of transgenic B. napus expressing a medium-chain thioesterase.
Learning Unsupervised Video Object Segmentation Through Visual Attention (2019)

This paper conducts a systematic study on the role of visual attention in Unsupervised Video Object Segmentation (UVOS) tasks. By elaborately annotating three popular video segmentation datasets (DAVIS, Youtube-Objects and SegTrack V2) with dynamic eye-tracking data in the UVOS setting, for the first time, we quantitatively verified the high consistency of visual attention behavior among human observers, and found strong correlation between human attention and explicit primary object judgements during dynamic, task-driven viewing. Such novel observations provide an in-depth insight into the underlying rationale behind UVOS. Inspired by these findings, we decouple UVOS into two sub-tasks: UVOS-driven Dynamic Visual Attention Prediction (DVAP) in spatiotemporal domain, and Attention-Guided Object Segmentation (AGOS) in spatial domain. Our UVOS solution enjoys three major merits: 1) modular training without using expensive video segmentation annotations, instead, using more affordable dynamic fixation data to train the initial video attention module and using existing fixation-segmentation paired static/image data to train the subsequent segmentation module; 2) comprehensive foreground understanding through multi-source learning; and 3) additional interpretability from the biologically-inspired and assessable attention. Experiments on popular benchmarks show that, even without using expensive video object mask annotations, our model achieves compelling performance in comparison with state-of-the-arts.
Camelliasaponins B1, B2, C1, and C2, New Type Inhibitors of Ethanol Absorption in Rats from the Seeds of Camellia japonica L.. (1994)

New type inhibitors of ethanol absorption, camelliasaponins B1, B2, C1 and C2, were isolated from the seeds of Camellia japonica L. The structures of camelliasaponins were elucidated on the basis of chemical and physicochemical evidence. The inhibitory effect of camelliasaponins and related saponins on ethanol absorption have been examined, and it was found that the triterpene oligoglycoside structure having an acyl group was essential to exerting the activity.
Microbiota-Targeted Therapies: An Ecological Perspective (2012)

Insights from ecology will help to drive the development of microbiota-targeted therapeutics.
Silylchalcogenolates MESiRtBu2 (M = Na, Cu, Zn, Fe; E = S, Se, Te; R = tBu, Ph) and Disilyldichalcogenides tBu2RSiE−ESiRtBu2 (E = S, Se, Te; R = tBu, Ph):  Synthesis, Properties, and Structures (2005)

The sodium silyl chalcogenolates NaESiR(t)Bu(2) (R = Ph, (t)Bu; E = S, Se, Te), accessible by the nucleophilic degradation of S, Se, or Te by the sodium silanides NaSiR(t)Bu(2) (R = Ph, (t)Bu), have been characterized by X-ray structure analysis. Protonolysis of the sodium silyl chalcogenolates yields the corresponding chalcogenols. The Cu and Zn chalcogenolates, [Cu(SSiPh(t)Bu(2))](4) and [ZnCl(SSi(t)Bu(3))(THF)](2), have been synthesized by metathesis reactions of CuCl with NaSSiPh(t)Bu(2) and of ZnCl(2) with NaSSi(t)Bu(3), respectively. The solid-state structures of the transition metal thiolates have been determined. The compounds (t)Bu(2)RSiE-ESiR(t)Bu(2) (R = Ph, (t)Bu; E = S, Se, Te) are accessible via air oxidation. With the exception of (t)Bu(3)SiS-SSi(t)Bu(3), these compounds were analyzed using X-ray crystallography and represent the first structurally characterized silylated heavy dichalcogenides. Oxidative addition of (t)Bu(3)SiTe-TeSi(t)Bu(3) to Fe(CO)(5) yields [Fe(TeSi(t)Bu(3))(CO)(3)](2), which has also been structurally characterized.
Reduced Cell Migration and Disruption of the Actin Cytoskeleton in Calpain-deficient Embryonic Fibroblasts (2001)

The physiological functions and substrates of the calcium-dependent protease calpain remain only partly understood. The mu- and m-calpains consist of a mu- or m-80-kDa large subunit (genes Capn1 and Capn2), and a common 28-kDa small subunit (Capn4). To assess the role of calpain in migration, we used fibroblasts obtained from Capn4(-/-) mouse embryos. The cells lacked calpain activity on casein zymography and did not generate the characteristic calpain-generated spectrin breakdown product that is observed in wild-type cells. Capn4(-/-) cells had decreased migration rates and abnormal organization of the actin cytoskeleton with a loss of central stress fibers. Interestingly, these cells extended numerous thin projections and displayed delayed retraction of membrane protrusions and filopodia. The number of focal adhesions was decreased in Capn4(-/-) cells, but the cells had prominent vinculin-containing focal complexes at the cell periphery. The levels of the focal adhesion proteins, alpha-actinin, focal adhesion kinase (FAK), spectrin, talin, and vinculin, were the same in Capn4(+/+) and Capn4(-/-) cells. FAK, alpha-actinin, and vinculin were not cleaved in either cell type plated on fibronectin. However, proteolysis of the focal complex component, talin, was detected in the wild-type cells but not in the Capn4(-/-) cells, suggesting that calpain cleavage of talin is important during cell migration. Moreover, talin cleavage was again observed when calpain activity was partially restored in Capn4(-/-) embryonic fibroblasts by stable transfection with a vector expressing the rat 28-kDa calpain small subunit. The results demonstrate unequivocally that calpain is a critical regulator of cell migration and of the organization of the actin cytoskeleton and focal adhesions.
Use of green fluorescent protein to visualize the early events of symbiosis between Rhizobium meliloti and alfalfa (Medicago sativa) (1996)

A gene encoding a variant of green fluorescent protein (GFP) of Aequorea victoria was put under the control of a promoter which is constitutive in Rhizobium meliloti. The heterologous GFP gene was expressed at high levels during all stages of symbiosis, allowing R. meliloti cells to be visualized as they grew in the rhizosphere, on the root surface, and inside infection threads. In addition, nodules that were infected with bacteria which were synthesizing GFP fluoresced when illuminated with blue light. GFP-tagged bacteria could be seen inside infection threads, providing the opportunity to measure the growth rate and determine the patterns of growth of R. meliloti residing inside its host plant.
A Robust Hand Tracking for Gesture-Based Interaction of Wearable Computers (2004)

Hand gesture-based interface is one of the most promising modes of natural and fluid human-computer interaction that substitutes for the mouse and keyboard in wearable computing systems. In wearable computing scenarios, hand positioning and tracking is particularly difficult due to complex background, lighting variation and image dithering caused by head movement. This paper proposes a robust hand tracking method for gesture-based interaction of a wearable computer with a visual helmet. The method is an extension of the basic CONDENSATION algorithm, which is able to track hand in dynamic and complex background. Furthermore, the algorithm can recognize the current hand gesture and automatically switch between multiple well-defined gesture templates in the tracking loop. The experimental results show that the proposed algorithm worked well in dynamic and complex background in real time.
BCL2A1 is a lineage-specific antiapoptotic melanoma oncogene that confers resistance to BRAF inhibition (2013)

Although targeting oncogenic mutations in the BRAF serine/threonine kinase with small molecule inhibitors can lead to significant clinical responses in melanoma, it fails to eradicate tumors in nearly all patients. Successful therapy will be aided by identification of intrinsic mechanisms that protect tumor cells from death. Here, we used a bioinformatics approach to identify drug-able, "driver" oncogenes restricted to tumor versus normal tissues. Applying this method to 88 short-term melanoma cell cultures, we show that the antiapoptotic BCL2 family member BCL2A1 is recurrently amplified in ∼30% of melanomas and is necessary for melanoma growth. BCL2A1 overexpression also promotes melanomagenesis of BRAF-immortalized melanocytes. We find that high-level expression of BCL2A1 is restricted to melanoma due to direct transcriptional control by the melanoma oncogene MITF. Although BRAF inhibitors lead to cell cycle arrest and modest apoptosis, we find that apoptosis is significantly enhanced by suppression of BCL2A1 in melanomas with BCL2A1 or MITF amplification. Moreover, we find that BCL2A1 expression is associated with poorer clinical responses to BRAF pathway inhibitors in melanoma patients. Cotreatment of melanomas with BRAF inhibitors and obatoclax, an inhibitor of BCL2A1 and other BCL2 family members, overcomes intrinsic resistance to BRAF inhibitors in BCL2A1-amplified cells in vitro and in vivo. These studies identify MITF-BCL2A1 as a lineage-specific oncogenic pathway in melanoma and underscore its role for improved response to BRAF-directed therapy.
Control of Heterologous Hepatitis C Virus Infection in Chimpanzees Is Associated with the Quality of Vaccine-Induced Peripheral T-Helper Immune Response (2003)

Prophylactic hepatitis C virus (HCV) vaccine trials with human volunteers are pending. There is an important need for immunological end points which correlate with vaccine efficacy and which do not involve invasive procedures, such as liver biopsies. By using a multicomponent DNA priming-protein boosting vaccine strategy, naïve chimpanzees were immunized against HCV structural proteins (core, E1, and E2) as well as a nonstructural (NS3) protein. Following immunization, exposure to the heterologous HCV 1b J4 subtype resulted in a peak of plasma viremia which was lower in both immunized animals. Compared to the naïve infection control and nine additional historical controls which became chronic, vaccinee 2 (Vac2) rapidly resolved the infection, while the other (Vac1) clearly controlled HCV infection. Immunization induced antibodies, peptide-specific gamma interferon (IFN-gamma), protein-specific lymphoproliferative responses, IFN-gamma, interleukin-2 (IL-2), and IL-4 T-helper responses in both vaccinees. However, the specificities were markedly different: Vac2 developed responses which were lower in magnitude than those of Vac1 but which were biased towards Th1-type cytokine responses for E1 and NS3. This proof-of-principle study in chimpanzees revealed that immunization with a combination of nonstructural and structural antigens elicited T-cell responses associated with an alteration of the course of infection. Our findings provide data to support the concept that the quality of the response to conserved epitopes and the specific nature of the peripheral T-helper immune response are likely pivotal factors influencing the control and clearance of HCV infection.
High performance transistors via aligned polyfluorene-sorted carbon nanotubes (2014)

We evaluate the performance of exceptionally electronic-type sorted, semiconducting, aligned single-walled carbon nanotubes (s-SWCNTs) in field effect transistors (FETs). High on-conductance and high on/off conductance modulation are simultaneously achieved at channel lengths which are both shorter and longer than individual s-SWCNTs. The s-SWCNTs are isolated from heterogeneous mixtures using a polyfluorene-derivative as a selective agent and aligned on substrates via dose-controlled, floating evaporative self-assembly at densities of ∼50 s-SWCNTs μm−1. At a channel length of 9 μm the s-SWCNTs percolate to span the FET channel, and the on/off ratio and charge transport mobility are 2.2 × 107 and 46 cm2 V−1 s−1, respectively. At a channel length of 400 nm, a large fraction of the s-SWCNTs directly span the channel, and the on-conductance per width is 61 μS μm−1 and the on/off ratio is 4 × 105. These results are considerably better than previous solution-processed FETs, which have suffered from poor on/off ratio due to spurious metallic nanotubes that bridge the channel. 4071 individual and small bundles of s-SWCNTs are tested in 400 nm channel length FETs, and all show semiconducting behavior, demonstrating the high fidelity of polyfluorenes as selective agents and the promise of assembling s-SWCNTs from solution to create high performance semiconductor electronic devices.
Immunization of Woodchucks with Plasmids Expressing Woodchuck Hepatitis Virus (WHV) Core Antigen and Surface Antigen Suppresses WHV Infection (1999)

DNA vaccination can induce humoral and cellular immune response to viral antigens and confer protection to virus infection. In woodchucks, we tested the protective efficacy of immune response to woodchuck hepatitis core antigen (WHcAg) and surface antigen (WHsAg) of woodchuck hepatitis virus (WHV) elicited by DNA-based vaccination. Plasmids pWHcIm and pWHsIm containing WHV c- or pre-s2/s genes expressed WHcAg and WHsAg in transient transfection assays. Pilot experiments in mice revealed that a single intramuscular injection of 100 microgram of plasmid pWHcIm DNA induced an anti-WHcAg titer over 1:300 that was enhanced by boost injections. However, two injections of 100 microgram of pWHcIm did not induce detectable anti-WHcAg in woodchucks. With an increase in the dose to 1 mg of pWHcIm per injection, transient anti-WHcAg response and WHcAg-specific proliferation of peripheral mononuclear blood cells (PMBCs) appeared in woodchucks after repeated immunizations. Four woodchucks vaccinated with pWHcIm were challenged with 10(4) or 10(5) of the WHV 50% infective dose. They remained negative for markers of WHV replication (WHV DNA and WHsAg) in peripheral blood and developed anti-WHs in week 5 after challenge. In contrast, woodchucks not immunized or immunized with the control vector pcDNA3 developed acute WHV infection. Two woodchucks immunized with 1 mg of pWHsIm developed WHsAg-specific proliferative response of PBMCs but no measurable anti-WHsAg response. A rapid anti-WHsAg response developed during week 2 after virus challenge. Neither woodchuck developed any signs of WHV infection. These data indicate that DNA-based vaccination with WHcAg and WHsAg can elicit immunity to WHV infection.
Induction of type I IFN is required for overcoming tumor-specific T-cell tolerance after stem cell transplantation (2009)

Tumor-specific T-cell tolerance represents one major mechanism of tumor-induced immune evasion. Myeloablative chemotherapy with stem cell transplantation may offer the best chance of achieving a state of minimal residual disease and, thus, minimize tumor-induced immune evasion. However, studies have shown that tumor-specific T-cell tolerance persists after transplantation. Here, we showed that CD4(+)CD25(+) regulatory T (T(Reg)) cells play a critical role in tumor-specific CD8(+) T-cell tolerance after transplantation. Removal of T(Reg) cells from the donor lymphocyte graft did not overcome this tolerance because of rapid conversion of donor CD4(+)CD25(-) T cells into CD4(+)CD25(+)Foxp3(+) T(Reg) cells in recipients after transplantation, and depletion of T(Reg) cells in recipients was necessary for the reversal of tumor-specific tolerance. These results suggest that strategies capable of overcoming T-cell tolerance in recipients are required to promote antitumor immunity after transplantation. Toward this goal, we showed that dendritic cell (DC) vaccines coadministered with the TLR9 ligand, CpG could effectively overcome tumor-specific tolerance, leading to significant prolongation of tumor-free survival after transplantation. We further showed that CpG-induced type I interferon was critical for the reversal of tumor-specific tolerance in vivo. Collectively, these results may suggest effective immunotherapeutic strategies for treating cancer after stem cell transplantation.
[Hand, foot and mouth disease--more than a harmless "childhood disease"]. (2014)

Hand, foot and mouth disease (HFMD) is a highly contagious, world-wide distributed viral illness that affects predominantly children. It is caused by several enteroviruses, such as coxsackieviruses A6, A10, A16 and enterovirus 71. In most cases, HFMD follows a benign and self-limiting course. After an incubation period of 3 to 10 days, fever and sore throat, the first symptoms of the disease, appear. A few days later, maculopapular or vesicular eruptions form on the palms and soles as well as in the oral cavity. Since the year 2000, several large HFMD outbreaks have been reported in many Asian regions such as China, Malaysia and Vietnam. In some of these outbreaks, high incidences of severe progressive HFMD forms with some fatalities were observed. Such diseases have been caused primarily by enterovirus 71 strains and were characterized frequently by sudden onset of fever, encephalitis/meningitis and severe respiratory symptoms such as pulmonary edema. Further severe neurological and cardiac complications have also been observed during these outbreaks. Recently, some HFMD outbreaks caused by the coxsackievirus A6 have been reported in several parts of the world. These illnesses also affected adults and were characterized by more severe symptoms of "classical" HFMD. In addition, outbreaks of coxsackievirus-A6-associated HFMD in many countries were associated with onychomadesis, with the loss of nails occurring up to two months after initial symptoms. Treatment of "classical" HFMD is usually symptomatic, a generally recommended antiviral therapy does not exist. In severe HFMD cases, suitable treatment also encompasses mechanical ventilation, as well as the additional application of antiviral agents such as ribavirin. In the last years, several novel agents with good in vitro and in vivo activity against enteroviruses have been developed. A vaccine against HFMD is not yet available.
The car Package (2006)

October 29, 2007 Version 1.2-7 Date 2007/10/27 Title Companion to Applied Regression Author John Fox . I am grateful to Douglas Bates, David Firth, Michael Friendly, Gregor Gorjanc, Spencer Graves, Richard Heiberger, Georges Monette, Henric Nilsson, Brian Ripley, Sanford Weisberg, and Achim Zeleis for various suggestions and contributions. Maintainer John Fox Depends R (>= 2.1.1), stats, graphics Suggests MASS, nnet, leaps LazyLoad yes LazyData yes Description This package accompanies J. Fox, An R and S-PLUS Companion to Applied Regression, Sage, 2002. The package contains mostly functions for applied regression, linear models, and generalized linear models, with an emphasis on regression diagnostics, particularly graphical diagnostic methods. There are also some utility functions. With some exceptions, I have tried not to duplicate capabilities in the basic distribution of R, nor in widely used packages. Where relevant, the functions in car are consistent with na.action = na.omit or na.exclude. License GPL (>= 2) URL http://www.r-project.org, http://socserv.socsci.mcmaster.ca/jfox/
A Wind Tunnel Model to Explore Unsteady Circulation Control for General Aviation Applications (2002)

Circulation Control airfoils have been demonstrated to provide substantial improvements in lift over conventional airfoils. The General Aviation Circular Control model is an attempt to address some of the concerns of this technique. The primary focus is to substantially reduce the amount of air mass flow by implementing unsteady flow. This paper describes a wind tunnel model that implements unsteady circulation control by pulsing internal pneumatic valves and details some preliminary results from the first test entry.
Localization of cardiac myosin-specific antibody in myocardial infarction. (1976)

Specific localization of purified antibody against cardiac myosin has been demonstrated in areas of altered myocardial membrane permeability after experimental myocardial infarction. Intravenously administered radioiodine-labeled antimyosin was selectively localized in infarcted myocardium of seven dogs 24 h after coronary occlusion. The mean ratio (+/-SE) of antimyosin antibody in infarcted to normal myocardium in the center of the infarct was 4.2+/-0.4 for endocardial and 2.9+/-0.3 for epicardial layers. By utilizing (Fab')2 fragments of antimyosin obtained by pepsin digestion of purified antibody, the ratio of uptake was increased in eight dogs to 6.1+/-0.6 in the endocardial and 3.3+/-0.4 in the epicardial layers at the infarct center 24 h after occlusion. These ratios were further increased in the infarct center to 13.8+/-1.2 in the endocardial and 7.3+/-0.8 in the epicardial layers when eight dogs were sacrificed 72 h after coronary occlusion. The specificity of antimyosin (Fab')2 localization in infarcted myocardium was demonstrated in four dogs by simultaneous intravenous administration of 125I-labeled antimyosin (Fab')2 and 131I-labeled normal rabbit gamma globulin (Fab')2. Nonspecific trapping of normal rabbit IgG (Fab')2 was observed to be about 38% of total antimyosin (Fab')2 uptake in the central zone of infarction. Regional blood flow was related to antimyosin (Fab')2 uptake in infarcted myocardium by utilizing simultaneous administration of 85Sr-labeled microspheres. An inverse exponential relationship between antimyosin (Fab')2 uptake and regional blood flow was observed (r=0.85). The specific localization of antimyosin antibody or its (Fab')2 components in infarcted myocardium suggests a conceptually new approach to myocardial infarct localization and sizing.
Smart Hydrogels Containing Adenylate Kinase: Translating Substrate Recognition into Macroscopic Motion (2008)

Enzyme-based hybrid hydrogels were prepared by covalently incorporating an adenylate kinase mutant, possessing two thiol groups, into HPMA copolymer- or PEG-based hydrogel structures. The nanoscale conformational change of enzyme, triggered by substrate recognition, translated into macroscopic motion of hydrogels.