gebhart/patrepeval huggingface dataset:
Monolignol ferulate conjugates are naturally incorporated into plant lignins (2016)

Angiosperms represent most of the terrestrial plants and are the primary research focus for the conversion of biomass to liquid fuels and coproducts. Lignin limits our access to fibers and represents a large fraction of the chemical energy stored in plant cell walls. Recently, the incorporation of monolignol ferulates into lignin polymers was accomplished via the engineering of an exotic transferase into commercially relevant poplar. We report that various angiosperm species might have convergently evolved to natively produce lignins that incorporate monolignol ferulate conjugates. We show that this activity may be accomplished by a BAHD feruloyl-coenzyme A monolignol transferase, <i>Os</i>FMT1 (AT5), in rice and its orthologs in other monocots.
Transfer RNA travels from the cytoplasm to organelles (2011)

Transfer RNAs (tRNAs) encoded by the nuclear genome are surprisingly dynamic. Although tRNAs function in protein synthesis occurring on cytoplasmic ribosomes, tRNAs can transit from the cytoplasm to the nucleus and then again return to the cytoplasm by a process known as the tRNA retrograde process. Subsets of the cytoplasmic tRNAs are also imported into mitochondria and function in mitochondrial protein synthesis. The numbers of tRNA species that are imported into mitochondria differ among organisms, ranging from just a few to the entire set needed to decode mitochondrially encoded mRNAs. For some tRNAs, import is dependent on the mitochondrial protein import machinery, whereas the majority of tRNA mitochondrial import is independent of this machinery. Although cytoplasmic proteins and proteins located on the mitochondrial surface participating in the tRNA import process have been described for several organisms, the identity of these proteins differ among organisms. Likewise, the tRNA determinants required for mitochondrial import differ among tRNA species and organisms. Here, we present an overview and discuss the current state of knowledge regarding the mechanisms involved in the tRNA retrograde process and continue with an overview of tRNA import into mitochondria. Finally, we highlight areas of future research to understand the function and regulation of movement of tRNAs between the cytoplasm and organelles.
Integrin traffic (2006)

Cell adhesion, migration and the maintenance of cell polarity are all processes that depend on the correct targeting of integrins and the dynamic remodelling of integrin-containing adhesion sites. The importance of the endo/exocytic cycle of integrins as a key regulator of these functions is increasingly recognized. Several recent publications have provided mechanistic insight into how integrin traffic is regulated in cells. Increasing evidence suggests that small GTPases such as Arf6 and members of the Rab family control integrin internalization and recycling back to the plasma membrane along microtubules. The fine tuning of these trafficking events seems to be mediated by specific guanine-nucleotide-exchange factors (GEFs) and GTPase-activating proteins (GAPs). In addition, several kinases regulate integrin traffic. The identification of their substrates has demonstrated how these kinases regulate integrin traffic by controlling small GTPases or stabilizing cytoskeletal tracks that are crucial for efficient traffic of integrins to the plasma membrane.
Common Genomic Variation in theAPOC3Promoter Associated With Variation in Plasma Lipoproteins (1997)

We hypothesized that common genomic variation that affected the expression and/or function of the products of the APOC3, APOE, FABP2, and PON1 genes would be associated with variation in biochemical phenotypes in a previously unstudied human sample. We determined genotypes of functional genomic variants of APOC3, APOE, FABP2, and PON1 in 509 adult aboriginal Canadians from an isolated community in Northern Ontario. We tested for genotype associations with plasma lipoprotein traits. We found that (1) common variation at nucleotide -455 of the APOC3 promoter was associated with variation in plasma triglycerides (P = .006) and (2) common variation of APOE determining plasma isoforms of apo E was associated with variation in plasma apo B (P = .009). Analysis of subjects classed by APOC3 markers showed that homozygosity for presence of a C at nucleotide -455 and a T at nucleotide -482 was associated with significantly increased plasma triglycerides in both men and women. Furthermore, this allele was approximately twice as frequent in subjects within the highest quartile of plasma triglycerides as in subjects within the lowest quartile. Since the DNA variation detected by the APOC3 markers affects in vitro expression of the gene product, it is possible that the marker itself caused the associations. However, the associations could also have resulted from linkage disequilibrium with other functional variants in APOC3 or the closely linked APOA1 and/or APOA4 genes.
Postresuscitation disease after cardiac arrest: a sepsis-like syndrome? (2004)

Postresuscitation abnormalities after cardiac arrest mimic the immunologic and coagulation disorders observed in severe sepsis. This suggests that therapeutic approaches used recently with success in severe sepsis should be investigated in patients successfully resuscitated after cardiac arrest.
Thermoreversible Organogels from Alkane Gelators with One Heteroatom (1999)

We have examined the abilities of five structurally simple molecules to form thermoreversible gels with a variety of organic liquids. Each gelator is an acyclic alkane with one heteroatom. Of these, dioctadecylamine (2N) is the most efficient gelator. At ≅3 wt % concentrations, it forms gels with alkanes, aromatic liquids, alkanols, methylene chloride, and silicone oil that are stable in closed containers at room temperature for >7 months. Each of the other moleculesoctadecylamine (1N), trioctadecylamine (3N), methyldioctadecylamine (MeN), and ditetradecylsulfide (2S)is able to gel at least silicone oil, and 3N and 2S also form stable gels with alkanols. The reason for the superiority of 2N as a gelator has been linked to its rodlike structure and ability to act as both a hydrogen-bond donor and hydrogen-bond acceptor. Evidence for the importance of H-bonding interactions in strands of the gels is found in infrared and differential scanning calorimetric measurements on the gelators in their neat and gelled phases and from comparisons of gelation temperatures. Some of the gels were examined also by polarized optical microscopy. These molecules are structurally among the simplest organogelators discovered to date. The fact that no more than one point of potentially strong interaction can exist between molecules in their assemblies requires a severe modification of current models for the necessary structural attributes of organogelators.
Selective striatal neuronal loss in a YAC128 mouse model of Huntington disease (2003)

An expanded CAG repeat is the underlying genetic defect in Huntington disease, a disorder characterized by motor, psychiatric and cognitive deficits and striatal atrophy associated with neuronal loss. An accurate animal model of this disease is crucial for elucidation of the underlying natural history of the illness and also for testing experimental therapeutics. We established a new yeast artificial chromosome (YAC) mouse model of HD with the entire human HD gene containing 128 CAG repeats (YAC128) which develops motor abnormalities and age-dependent brain atrophy including cortical and striatal atrophy associated with striatal neuronal loss. YAC128 mice exhibit initial hyperactivity, followed by the onset of a motor deficit and finally hypokinesis. The motor deficit in the YAC128 mice is highly correlated with striatal neuronal loss, providing a structural correlate for the behavioral changes. The natural history of HD-related changes in the YAC128 mice has been defined, demonstrating the presence of huntingtin inclusions after the onset of behavior and neuropathological changes. The HD-related phenotypes of the YAC128 mice show phenotypic uniformity with low inter-animal variability present, which together with the age-dependent striatal neurodegeneration make it an ideal mouse model for the assessment of neuroprotective and other therapeutic interventions.
Job stress, job strain, and psychological withdrawal among Dutch university staff: Towards a dualprocess model for the effects of occupational stress (2001)

This study examined the antecedents of job strain (emotional exhaustion, health complaints) and withdrawal behaviour (e.g. lowered organizational commitment) among a cross-sectional sample of 131 academic staff members of the law department of a large Dutch university. Conservation of resources theory (Hobfoll, 1989) provided the theoretical background for this study. Strains and withdrawal behaviours were expected to be most prominent among those who reported having few resources and/or who reported high job demands. Structural equation modelling revealed that this was indeed the case. As predicted, differential patterns of effects emerged for job demands and job resources. Analysis of the effects of four job-specific stressors revealed that especially the structural aspects of a staff member's teaching task (e.g. the number of students in their classes) contributed strongly to perceived job demands. Theoretical and practical implications of the study are discussed. Keywords: BurnoutUniversity StaffConservation Of ResourcesDemand-CONTROL ModelWell-BEINGTeachers Stress
Activity of compound G2 isolated from alfalfa roots against medically important yeasts (1986)

An antimycotic agent was isolated from roots of alfalfa and further purified to yield a nonhemolytic, homogeneous compound (G2). This compound contained considerable activity against 10 medically important yeasts. MICs obtained by both agar and broth dilution methods ranged from 3 to 15 micrograms/ml. Compound G2 was fungicidal at a relatively low concentration for nine different species of yeasts tested (minimum fungicidal concentrations ranged between 6 and 24 micrograms/ml). The considerable stability of compound G2 and its strong inhibitory and fungicidal activity against a broad range of yeasts suggest that after further development it might be useful as an active agent in the treatment of mycotic infections.
Apoptosis induced by methylene‐blue‐mediated photodynamic therapy in melanomas and the involvement of mitochondrial dysfunction revealed by proteomics (2008)

Methylene blue (MB) is a widely studied agent currently under investigation for its properties relating to photodynamic therapy (PDT). Recent studies have demonstrated that MB exhibits profound phototoxicity affecting a variety of tumor cell lines. However, the mechanistic explanation for methylene-blue-mediated photodynamic therapy (MB-PDT) in the context of melanoma therapy is still obscure. In the present study, B16F1 melanoma cells were treated by MB-PDT under different conditions, and thereafter subjected to cell viability detection assays. MB-PDT could induce intense apoptotic cell death through a series of steps beginning with the photochemical generation of reactive oxygen species that activate the caspase-9/caspase-3 apoptosis pathway. Blocking activation of caspase-3 and induction of oxidative stress by caspase inhibitor and by glutathione, respectively, markedly reduced apoptotic cell death in vitro. Importantly, proteomics study defining altered protein expression in treated cells suggests the involvement of several mitochondrial proteins playing important roles in electron transfer chain, implying mitochondrial dysfunction during the treatment. Furthermore, a transplantable mouse melanoma model was utilized to estimate the effectiveness of MB-PDT in vivo. The treated mice displayed decreased tumor size and prolonged survival days, which was associated with enhanced apoptotic cell death. These results, offering solid evidence of the induction of mitochondria-related apoptosis in tumor cells, reveal new aspects of MB-PDT having potential to be a palliative treatment of melanoma.
Transgenic mice that express Cre recombinase under control of a skeletal muscle-specific promoter frommef2c (2005)

Genes expressed in skeletal muscle are often required in other tissues. This is particularly the case for cardiac and smooth muscle, both contractile tissues that share numerous characteristics with skeletal muscle, such that targeted inactivation can lead to embryonic lethality prior to a requirement for gene function in skeletal muscle. Thus, it is essential that conditional inactivation approaches are developed to disrupt genes specifically in skeletal muscle. In this report, we describe a transgenic mouse that expresses Cre recombinase under the control of a skeletal muscle-specific promoter from the mef2c gene. Cre expression in this transgenic line is completely restricted to skeletal muscle from early in development and is present in all skeletal muscles, including those of epaxial and hypaxial origins and in fast and slow fibers. This early skeletal muscle-specific Cre line will be a useful tool to define the function of genes specifically in skeletal muscle.
A Phase I Safety and Pharmacokinetic Study of the Death Receptor 5 Agonistic Antibody PRO95780 in Patients with Advanced Malignancies (2010)

PRO95780 is safe and well tolerated at doses up to 20 mg/kg. Evidence of activity was noted in several different tumor types at 4 and 10 mg/kg. Pharmacokinetic analysis supports a dosing regimen of 10 to 15 mg/kg every 2 to 3 weeks.
Theory of 1/T1 and 1/T2 NMRD profiles of solutions of magnetic nanoparticles (1995)

Organically coated iron oxide crystallites with diameters of 5-50 nm ("nanoparticles") are potential magnetic resonance imaging contrast agents. 1/T1 and 1/T2 of solvent water protons are increased dramatically by magnetic interactions in the "outer sphere" environment of the nanoparticles; subsequent diffusive mixing distributes this relaxation throughout the solvent. Published theory, valid for the solute magnetic energy small compared with thermal energy, is applicable to small magnetic solutes (e.g., gadolinium and manganese diethylenetriaminopentaacetic acid, and nitroxide free radicals) at generally accessible fields (< or = 50 T). It fails for nanoparticles at fields above approximately 0.05 T, i.e., at most imaging fields. The authors have reformulated outer sphere relaxation theory to incorporate progressive magnetic saturation of solute nanoparticles and, in addition, indicate how to use empirical magnetization data for realistic particles when their magnetic properties are not ideal. It is important to handle the effects of rapid thermally induced reorientation of the magnetization of the nanoparticles (their "superparamagnetism") effectively, including their sensitivity to particle size. The theoretical results are presented as the magnetic field dependence (NMRD profiles) of 1/T1 and 1/T2, normalized to Fe content, for three sizes of particles, and then compared with the limited data extant for well-characterized material.
Synthesis and Direct Imaging of Ultrahigh Molecular Weight Cyclic Brush Polymers (2011)

Convenient route to cyclic polymers: Ultrahigh molecular weight cyclic brush polymers were synthesized through ring-expansion metathesis polymerization of various macromonomers. Atomic force microscopy was used to visualize toroidal shapes and large opening pores, along with linear chains, which may result from high sensitivity of brush polymers to mechanical degradation.
A phase 1 study of the PI3Kδ inhibitor idelalisib in patients with relapsed/refractory mantle cell lymphoma (MCL) (2014)

Idelalisib, an oral inhibitor of phosphatidylinositol-3-kinase δ (PI3Kδ), was evaluated in a 48-week phase 1 study (50-350 mg daily or twice daily) enrolling 40 patients with relapsed or refractory mantle cell lymphoma (MCL). Primary outcome was safety and dose-limiting toxicity (DLT). Secondary outcomes were pharmacokinetic parameters, pharmacodynamic effects, overall response rate (ORR), progression-free survival (PFS), and duration of response (DOR). Patients without DLT and no evidence of disease progression after 48 weeks enrolled in the extension study. Patients had median age of 69 years (range, 52-83) and received median of 4 prior therapies (1-14); 17 of 40 patients (43%) were refractory to their most recent treatment. Median duration of idelalisib treatment was 3.5 months (range, 0.7-30.7), with 6 (15%) continuing extension treatment. Common grade ≥3 adverse events (AEs) included (total%/grade ≥3%) diarrhea (40/18), nausea (33/5), pyrexia (28/0), fatigue (25/3), rash (23/3), decreased appetite (20/15), upper respiratory infection (20/0), pneumonia (13/10), and alanine transaminase or aspartate transaminase elevations (60/20). ORR was 16 of 40 patients (40%), with CR in 2 of 40 patients (5%). Median DOR was 2.7 months, median PFS was 3.7 months, and 1-year PFS was 22%. These data provide proof of concept that targeting PI3Kδ is a viable strategy and worthy of additional study in MCL. This trial was registered at www.clinicaltrials.gov as #NCT00710528.
NaKtide, a Na/K-ATPase-derived Peptide Src Inhibitor, Antagonizes Ouabain-activated Signal Transduction in Cultured Cells (2009)

We have previously shown that the Na/K-ATPase binds and inhibits Src. Here, we report the molecular mechanism of Na/K-ATPase-mediated Src regulation and the generation of a novel peptide Src inhibitor that targets the Na/K-ATPase/Src receptor complex and antagonizes ouabain-induced protein kinase cascades. First, the Na/K-ATPase inhibits Src kinase through the N terminus of the nucleotide-binding domain of the alpha1 subunit. Second, detailed mapping leads to the identification of a 20-amino acid peptide (NaKtide) that inhibits Src (IC50 = 70 nm) in an ATP concentration-independent manner. Moreover, NaKtide does not directly affect the ERK and protein kinase C family of kinases. It inhibits Lyn with a much lower potency (IC50 = 2.5 microm). Third, highly positively charged leader peptide conjugates including HIV-Tat-NaKtide (pNaKtide) readily enter cultured cells. Finally, the following functional studies of pNaKtide demonstrate that this conjugate can specifically target the Na/K-ATPase-interacting pool of Src and act as a potent ouabain antagonist in cultured cells: 1) pNaKtide, unlike PP2, resides in the membranes. Consistently, it affects the basal Src activity much less than that of PP2. 2) pNaKtide is effective in disrupting the formation of the Na/K-ATPase/Src receptor complex in a dose-dependent manner. Consequently, it blocks ouabain-induced activation of Src, ERK, and hypertrophic growth in cardiac myocytes. 3) Unlike PP2, pNaKtide does not affect IGF-induced ERK activation in cardiac myocytes. Taken together, we suggest that pNaKtide may be used as a novel antagonist of ouabain for probing the physiological and pathological significance of the newly appreciated signaling function of Na/K-ATPase and cardiotonic steroids.
Effects of Astragalus Injection on left cardiac function in elderly patients with acute myocardial infarction (2003)

AIM: To evaluate effects of Astragalus Injection on left cardiac function in elderly patients with acute myocardial infarction (AMI). METHODS: 92 elderly patients with AMI were randomly divided into Astragalus Injection treatment group and control group. The cardiac systolic and diastolic functions were assessed by nuclide gating cardiac blood-pool imaging in all patients after 4 wk treatment. All patients were followed up for 8th week after infarction. RESULTS: Compared with control group, left ventricular ejection fraction (LVEF), left ventricular peak ejecting rate (PER) and left ventricular peak filling rate (PFR) were higher,and left ventricular time for peck filling rate (TPFR) was shorter in treatment group. The attack rate of angina pectoris was lower slightly in treatment group, but not significantly than that in control group. NYHA classes were lower in treatment group, and the difference of NYHA class between two groups had significance (P= 0.0025 ). CONCLUSION: Astragalus Injection is an effective drug in improving left cardiac function in elderly patients with AMI.
HIV-1-Specific Antibody Response and Function after DNA Prime and Recombinant Adenovirus 5 Boost HIV Vaccine in HIV-Infected Subjects (2016)

Little is known about the humoral immune response against DNA prime-recombinant adenovirus 5 (rAd5) boost HIV vaccine among HIV-infected patients on long-term suppressive antiretroviral therapy (ART). Previous studies emphasized cellular immune responses; however, current research suggests both cellular and humoral responses are likely required for a successful therapeutic vaccine. Thus, we aimed to understand antibody response and function induced by vaccination of ART-treated HIV-1-infected patients with immune recovery. All subjects participated in EraMune 02, an open-label randomized clinical trial of ART intensification followed by a six plasmid DNA prime (envA, envB, envC, gagB, polB, nefB) and rAd5 boost HIV vaccine with matching inserts. Antibody binding levels were determined with a recently developed microarray approach. We also analyzed neutralization efficiency and antibody-dependent cellular cytotoxicity (ADCC). We found that the DNA prime-rAd5 boost vaccine induced a significant cross-clade HIV-specific antibody response, which correlated with antibody neutralization efficiency. However, despite the increase in antibody binding levels, the vaccine did not significantly stimulate neutralization or ADCC responses. This finding was also reflected by a lack of change in total CD4+ cell associated HIV DNA in those who received the vaccine. Our results have important implications for further therapeutic vaccine design and administration, especially in HIV-1 infected patients, as boosting of preexisting antibody responses are unlikely to lead to clearance of latent proviruses in the HIV reservoir.
Hemoglobin degradation in the human malaria pathogen Plasmodium falciparum: a catabolic pathway initiated by a specific aspartic protease. (1991)

Hemoglobin is an important nutrient source for intraerythrocytic malaria organisms. Its catabolism occurs in an acidic digestive vacuole. Our previous studies suggested that an aspartic protease plays a key role in the degradative process. We have now isolated this enzyme and defined its role in the hemoglobinolytic pathway. Laser desorption mass spectrometry was used to analyze the proteolytic action of the purified protease. The enzyme has a remarkably stringent specificity towards native hemoglobin, making a single cleavage between alpha 33Phe and 34Leu. This scission is in the hemoglobin hinge region, unraveling the molecule and exposing other sites for proteolysis. The protease is inhibited by pepstatin and has NH2-terminal homology to mammalian aspartic proteases. Isolated digestive vacuoles make a pepstatin-inhibitable cleavage identical to that of the purified enzyme. The pivotal role of this aspartic hemoglobinase in initiating hemoglobin degradation in the malaria parasite digestive vacuoles is demonstrated.
Learning symmetry groups with hidden units: Beyond the perceptron (1986)

Learning to recognize mirror, rotational and translational symmetries is a difficult problem for massively-parallel network models. These symmetries cannot be learned by first-order perceptrons or Hopfield networks, which have no means for incorporating additional adaptive units that are hidden from the input and output layers. We demonstrate that the Boltzmann learning algorithm is capable of finding sets of weights which turn hidden units into useful higher-order feature detectors capable of solving symmetry problems.