gebhart/patrepeval huggingface dataset:
Killing Epstein-Barr Virus-Positive B Lymphocytes by Gene Therapy: Comparing the Efficacy of Cytosine Deaminase and Herpes Simplex Virus Thymidine Kinase (1996)

Epstein-Barr virus (EBV)-positive lymphomas are frequent among immunosuppressed patients. We have examined the feasibility of killing EBV-immortalized B lymphocytes by gene transfer involving the use of "suicide" genes whose expression in target cells renders them susceptible to killing by a prodrug. We examined two gene/prodrug pairs: the Escherichia coli cytosine deaminase (CD) gene with the prodrug 5-fluorocytosine (5-FC), and the herpes simplex virus thymidine kinase (HSV-TK) gene with the prodrug ganciclovir. Retroviral vectors and drug selection were used to obtain CD or HSV-TK expression in cells. Both the CD/5-FC and the HSV-TK/ganciclovir combinations yielded substantial killing of EBV-immortalized B lymphocytes in vitro, although the CD/5-FC regimen had a significantly greater therapeutic margin than the HSV-TK/ganciclovir combination. The CD/5-FC pair, but not the HSV-TK/ganciclovir pair, was shown to have a "bystander killing effect" in vitro. When only 30% of the cells expressed the suicide gene, scid mouse tumors regressed in both the CD/5-FC regimen and the HSV-TK/ganciclovir regimen, documenting an in vivo bystander effect with both regimens. However, a greater percentage of tumors completely regressed with the CD/5-FC regimen. Overall, the sum of our data indicates that the CD/5-FC combination is the more promising regimen for treatment of EBV-associated lymphomas in vivo.
Muscle damage induced by eccentric contractions of 25% strain (1991)

Contractile and morphological properties were measured in the rabbit tibialis anterior muscle 1 h after isometric contraction (IC), passive stretch (PS), or eccentric contraction (EC). Maximal tetanic tension (Po) was reduced after 30 min of PS (P less than 0.001), IC (P less than 0.001), or EC (P less than 0.0001). However, the magnitude of the force deficit was a function of the treatment method. After 30 min of cyclic PS, Po decreased by 13%, whereas after IC or EC, Po decreased by 31 and 69%, respectively. The time course of tension decline in the various groups suggested that the EC-induced injury occurred during the first few minutes of treatment. Although the morphology of samples from the PS and IC groups appeared normal, eccentrically exercised muscles exhibited portions of abnormally large fibers (diam greater than or equal to 110 microns) when viewed in cross section. Examination of 231 such fibers from 6 muscles revealed that all enlarged fibers were exclusively of the fast-twitch glycolytic fiber type. Although no ultrastructural abnormalities were observed in any of the muscles from the IC or PS groups, a significant portion of the fibers in the EC group displayed various degrees of disorganization of the sarcomeric band pattern. Taken together, these studies highlight the importance of fiber oxidative capacity in EC-induced injury, which may be related to the damage mechanism.
Antibody-Mediated Enhancement of Human Immunodeficiency Virus Type 1 Infectivity Is Determined by the Structure of gp120 and Depends on Modulation of the gp120-CCR5 Interaction (2002)

In this study, we characterized the viral determinants of coreceptor usage in relation to susceptibility to antibody-mediated neutralization or enhancement of infectivity by using chimeras of three highly related human immunodeficiency virus type 1 (HIV-1) isolates of different phenotypes. We found that the V3 region was the main determinant of antibody-mediated enhancement and coreceptor specificity but that the overall structure of gp120 was also important for these properties. Constructs susceptible to antibody-mediated enhancement preferentially use CCR5 as a coreceptor, in contrast to constructs that were neutralized or not affected. Using monoclonal antibodies directed against CD4 or CCR5, we were able to show that antibody-mediated enhancement was CD4 dependent. Altogether, our results suggest that the modulation of the interaction of gp120 with CCR5 is the mechanism underlying antibody-mediated enhancement of HIV-1 infectivity.
Longitudinal Analysis of the Premature Infant Intestinal Microbiome Prior to Necrotizing Enterocolitis: A Case-Control Study (2015)

Necrotizing enterocolitis (NEC) is an inflammatory disease of the newborn bowel, primarily affecting premature infants. Early intestinal colonization has been implicated in the pathogenesis of NEC. The objective of this prospective case-control study was to evaluate differences in the intestinal microbiota between infants who developed NEC and unaffected controls prior to disease onset. We conducted longitudinal analysis of the 16S rRNA genes of 312 samples obtained from 12 NEC cases and 26 age-matched controls with a median frequency of 7 samples per subject and median sampling interval of 3 days. We found that the microbiome undergoes dynamic development during the first two months of life with day of life being the major factor contributing to the colonization process. Depending on when the infant was diagnosed with NEC (i.e. early vs. late onset), the pattern of microbial progression was different for cases and controls. The difference in the microbiota was most overt in early onset NEC cases and controls. In proximity to NEC onset, the abundances of Clostridium sensu stricto from Clostridia class were significantly higher in early onset NEC subjects comparing to controls. In late onset NEC, Escherichia/Shigella among Gammaproteobacteria, showed an increasing pattern prior to disease onset, and was significantly higher in cases than controls six days before NEC onset. Cronobacter from Gammaproteobacteria was also significantly higher in late onset NEC cases than controls 1-3 days prior to NEC onset. Thus, the specific infectious agent associated with NEC may vary by the age of infant at disease onset. We found that intravenously administered antibiotics may have an impact on the microbial diversity present in fecal material. Longitudinal analysis at multiple time points was an important strategy utilized in this study, allowing us to appreciate the dynamics of the premature infant intestinal microbiome while approaching NEC at various points.
Relationship between small antisense RNAs and aberrant RNAs associated with sense transgene mediated gene silencing in tomato (2002)

We investigated the occurrence and properties of small sense and antisense RNAs and aberrant transcripts in transgenic tomato plants exhibiting post-transcriptional silencing of the endogenous polygalacturonase (PG) sense gene and a truncated homologous transgene. Small antisense RNAs, about 23 nucleotides in size, were present in the leaves and immature green fruit where the transgene was transcribed in the absence of transcripts from the fruit ripening-specific endogenous PG gene. This suggests that the small antisense RNAs were produced from the transgene, which was supported by their failure to hybridise with the 3' half of the endogenous PG gene, the region that was excluded from the transgene. The features of two aberrant RNAs, corresponding to the 5' and 3' halves of the endogenous gene, strongly suggest that they arise by endonucleolytic cleavage of endogenous PG mRNA. The region where cleavage occurs is associated with the preferential production of small RNAs from the 3' end of the transgene. These results suggest a model where small antisense RNAs generated from the 3' end of the transgene anneal to the endogenous mRNA, resulting in cleavage at or near the annealing regions.
Better prediction of protein cellular localization sites with the k nearest neighbors classifier. (1997)

We have compared four classifiers on the problem of predicting the cellular localization sites of proteins in yeast and E. coli. A set of sequence derived features, such as regions of high hydrophobicity, were used for each classifier. The methods compared were a structured probabilistic model specifically designed for the localization problem, the k nearest neighbors classifier, the binary decision tree classifier, and the naïve Bayes classifier. The result of tests using stratified cross validation shows the k nearest neighbors classifier to perform better than the other methods. In the case of yeast this difference was statistically significant using a cross-validated paired t test. The result is an accuracy of approximately 60% for 10 yeast classes and 86% for 8 E. coli classes. The best previously reported accuracies for these datasets were 55% and 81% respectively.
Securing powerline communications (2008)

Powerline Communications represents an exceptionally promising alternative for high-speed Internet access and data networking. Its strength and popularity can be attributed to its ubiquitous nature and readily available infrastructure. Multiple applications are envisioned and powerlines have become increasing popular choice for creating residential networks. This communication medium has been well studied and standardization of the technologies are undergoing. However, the security aspects of PLC networks are not well studied and there is an urgent need for that. In this paper, we put forth several security requirements needed of PLC networks and justify them through multiple scenarios. We then propose a Security Architecture to realize these requirements.
Phosphorylation of Angiomotin by Lats1/2 Kinases Inhibits F-actin Binding, Cell Migration, and Angiogenesis (2013)

The Hippo tumor suppressor pathway plays important roles in organ size control through Lats1/2 mediated phosphorylation of the YAP/TAZ transcription co-activators. However, YAP/TAZ independent functions of the Hippo pathway are largely unknown. Here we report a novel role of the Hippo pathway in angiogenesis. Angiomotin p130 isoform (AMOTp130) is phosphorylated on a conserved HXRXXS motif by Lats1/2 downstream of GPCR signaling. Phosphorylation disrupts AMOT interaction with F-actin and correlates with reduced F-actin stress fibers and focal adhesions. Furthermore, phosphorylation of AMOT by Lats1/2 inhibits endothelial cell migration in vitro and angiogenesis in zebrafish embryos in vivo. Thus AMOT is a direct substrate of Lats1/2 mediating functions of the Hippo pathway in endothelial cell migration and angiogenesis.
Low-density lipoprotein receptor binding determinants switch from apolipoprotein E to apolipoprotein B during conversion of hypertriglyceridemic very-low-density lipoprotein to low-density lipoproteins. (1984)

Using thrombin and trypsin as probes, we determined: first, that low-density lipoprotein (LDL) receptor binding determinants switch from apolipoprotein (apo) E to apo-B within the very-low-density lipoprotein (VLDL) Sf 20-60 region of the metabolic cascade from VLDL1 (Sf 100-400) of hypertriglyceridemic (HTG) human subjects to LDL. Second, two different conformations of apo-E exist in HTG-VLDL Sf greater than 60, one accessible (greater than or equal to 1 mol/mol of particle) and one inaccessible (1-2 mol/mol) to both thrombin and the LDL receptor; normal VLDL (Sf greater than 60) have only the inaccessible conformation and therefore do not bind to the LDL receptor. Third, thrombin degrades apo-B into large fragments, three of which have electrophoretic mobilities similar to B-48, B-74, and B-26; this, however, has no effect on apo-B-mediated receptor binding. Fibroblast studies showed that thrombin could abolish receptor uptake of HTG-VLDL1 and HTG-VLDL2 (Sf 60-100), had little or no effect on HTG-VLDL3 (Sf 20-60), and no effect on uptake of intermediate-density lipoprotein (IDL) or LDL. Trypsin abolished the binding of HTG-VLDL1 and HTG-VLDL2, reduced that of HTG-VLDL3, but had little to no effect on IDL or LDL binding. Immunochemical techniques revealed that thrombin cleaved some apo-E into the E-22 and E-12 fragments; after trypsin treatment no apo-E was detected in any HTG-lipoprotein. Normal VLDL subclasses contained less apo-E than the corresponding HTG-VLDL subclasses and it was not cleaved by thrombin. Apo-B immunoreactivities of VLDL subclasses were not significantly changed after treatment with thrombin, although thrombin cleaved some of the B-100 of each VLDL subclass, and all apo-B in IDL and LDL, into 4-6 major large fragments. Trypsin converted all of the apo-B of each lipoprotein into smaller fragments (Mr less than 100,000). We conclude that apo-E of the thrombin-accessible conformation mediates uptake of HTG-VLDL1 and HTG-VLDL2 but that apo-B alone is sufficient to mediate receptor binding of IDL and LDL; the switch from apo-E to apo-B as the primary or sufficient binding determinant occurs within the VLDL3 (Sf 20-60) region of the metabolic cascade, where receptor binding first appears in VLDL subclasses from normal subjects.
A Calcium-Regulated MEF2 Sumoylation Switch Controls Postsynaptic Differentiation (2006)

Postsynaptic differentiation of dendrites is an essential step in synapse formation. We report here a requirement for the transcription factor myocyte enhancer factor 2A (MEF2A) in the morphogenesis of postsynaptic granule neuron dendritic claws in the cerebellar cortex. A transcriptional repressor form of MEF2A that is sumoylated at lysine-403 promoted dendritic claw differentiation. Activity-dependent calcium signaling induced a calcineurin-mediated dephosphorylation of MEF2A at serine-408 and, thereby, promoted a switch from sumoylation to acetylation at lysine-403, which led to inhibition of dendritic claw differentiation. Our findings define a mechanism underlying postsynaptic differentiation that may modulate activity-dependent synapse development and plasticity in the brain.
Reallocation of system mass and stiffness for achieving target specifications (2004)

The development of a system model involves the assemblage of many important components from a dynamic standpoint. The performance of the system is dependent on the dynamic characteristics of each of the components. In an attempt to improve the overall system characteristics, targets are typically specified at the system level. The determination of the component characteristics to achieve these targets are the purpose of this work. Using these targets, an inverse optimisation process can be utilised to determine the adjustment of the mass and stiffness of the system. However, the inverse process will smear the mass and stiffness over all the system degrees of freedom unless all the system equations are utilised in the inverse process or unless some constraints are applied to the set of equations. This smearing tends to confuse the proper mass and stiffness that are needed to achieve the design targets to meet the desired component dynamic characteristics. This work utilises analytical model improvement techniques along with localisation of model change procedures to determine the component target characteristics. As part of the procedure, the existing topology of the finite element model can be modified to restrict or allow additional elemental connectivities in the optimisation process.
Improving the characteristics of a transducer using multiple piezoelectric layers (1993)

A type of transducer composed of several active piezoelectric layers is described. These layers are independently stimulated electrically to achieve performance, in terms of sensitivity and bandwidth, not available in conventional, single active layer designs. A straightforward modeling technique is employed for predicting the performance of these transducers and for determining the optimal excitation characteristics. The technique is initially developed for transmission, but its extension to reception and pulse-echo conditions is discussed. A selection of experimental results demonstrates the feasibility of the technique.
Development and Characterization of Mouse Hybridomas (2007)

Cell fusion protocols that were developed by Kohler and Milstein in the mid-1970s and aimed at producing and characterization of mouse monoclonal antibodies (MAbs) remain the gold standard of hybridoma development. Despite tremendous progress in using MAbs in multiple research, diagnostic, and therapeutic areas, major experimental flaws in designing and carrying out hybridoma experimentation often result in the production of hybridomas exhibiting poor growth parameters and secreting low-specificity and low-affinity antibodies. This methodology chapter is built around the conventional hybridoma protocol, with a special emphasis on tissue culture and biochemical techniques aimed at producing truly monospecific and highly active mouse MAbs.
THE REASON FOR THE SHAPE OF THE DISTENSIBILITY CURVES OF ARTERIES (1957)

It is characteristic of arteries that they do not obey Hooke's law, but resist further stretch more strongly, the more they are stretched. It appears that this might be due to the combination of elastin fibers in the elastic laminae, with the much less distensible collagenous libers in the media and adventitia, more and more of which reach their 'unstretched length' as distension is increased. This has been verified on human iliac arteries, from autopsy, by comparing the 'elastic diagrams' (tension vs. circumference) before and after differential digestion of collagen by formic acid, and digestion of elastin by crude trypsin (containing an elastase). This proved that the resistance to stretch at low pressures was almost entirely due to elastin fibers, that at physiological pressures due to both collagenous and elastin fibers, but dominantly to collagen, and that at high pressures almost entirely due to collagenous fibers. In future work on the effect of age on the elasticity of iliac arteries, the initial slope of the elastic diagram can be taken as an index of the state, or number, of the elastin fibers, and the final slope as an index of the state, or number, of collagenous fibers.
The American College of Rheumatology criteria for the classification of systemic lupus erythematosus: Strengths, weaknesses, and opportunities for improvement (1999)

The American College of Rheumatology classification criteria were developed to operationalize the definition of systemic lupus erythematosus (SLE) to allow comparison of clinical research from different centers, but also serve to facilitate education and to guide clinical practice. The classification criteria have been critical to research, but should be viewed as a temporary step until improved understanding of the pathogenesis of SLE emerges. Criteria have inherent limitations, including bias towards more severe and longer duration disease, equal weighting of features that vary in clinical significance, and exclusion of patients with SLE from research because they do not meet criteria. For some SLE research questions, it may be appropriate to include patients diagnosed with SLE who do not meet criteria, if these patients' manifestations and criteria are documented explicitly. SLE disease activity, cumulative organ damage, disease duration, criteria ever met, and criteria met at time of enrollment are important data that should be presented in clinical studies of SLE regardless of the number of criteria met. The criteria should be reevaluated periodically, utilizing patients and controls with a range of diseases and disease severity. A simplified weighting system may more accurately reflect clinical practice.
The A/Mallard/67S0/78 Avian-Human, but Not the A/Ann Arbor/6/60 Cold-Adapted, Influenza A/Kawasaki/86 (H1N1) Reassortant Virus Vaccine Retains Partial Virulence for Infants and Children (1991)

Characteristics of avian-human (ah) and cold-adapted (ca) influenza A/Kawasaki/9/86 (H1N1) reassortant vaccine viruses were compared in 37 seronegative adults and 122 seronegative infants and children. The 50% human infectious dose (HID50) in infants and children was 10(2.9) and 10(2.6) TCID50 for the ah and ca vaccine, respectively. The ah influenza A/Kawasaki/9/86 reassortant was reactogenic: 24% of infants and children infected with greater than or equal to 100 HID50 had fever greater than or equal to 39.4 degrees C. Since H3N2 ah vaccines were previously shown to be adequately attenuated, it is reasonable to suggest that the genes that code for hemagglutinin and neuraminidase of the H1N1 virus apparently influence the reactogenicity of reassortant viruses derived from the avian influenza A/Mallard/New York/6750/78 donor virus. Because this avian virus does not reproducibly confer a satisfactory level of attenuation to each subtype of influenza A virus, it is not a suitable donor virus for attenuation of wild-type influenza viruses. In contrast, the ca A/Ann Arbor/6/60 donor virus reliably confers attenuation characteristics to a variety of H1N1 and H3N2 influenza A viruses.
Neuroprotection by flavonoids (2003)

The high morbidity, high socioeconomic costs and lack of specific treatments are key factors that define the relevance of brain pathology for human health and the importance of research on neuronal protective agents. Epidemiological studies have shown beneficial effects of flavonoids on arteriosclerosis-related pathology in general and neurodegeneration in particular. Flavonoids can protect the brain by their ability to modulate intracellular signals promoting cellular survival. Quercetin and structurally related flavonoids (myricetin, fisetin, luteolin) showed a marked cytoprotective capacity in in vitro experimental conditions in models of predominantly apoptotic death such as that induced by medium concentrations (200 M) of H2O2 added to PC12 cells in culture. Nevertheless, quercetin did not protect substantia nigra neurons in vivo from an oxidative insult (6-hydroxydopamine), probably due to difficulties in crossing the blood-brain barrier. On the other hand, treatment of permanent focal ischemia with a lecithin/quercetin preparation decreased lesion volume, showing that preparations that help to cross the blood-brain barrier may be critical for the expression of the effects of flavonoids on the brain. The hypothesis is advanced that a group of quercetin-related flavonoids could become lead molecules for the development of neuroprotective compounds with multitarget anti-ischemic effects.
Intravenous glial‐derived neurotrophic factor gene therapy of experimental Parkinson's disease with Trojan horse liposomes and a tyrosine hydroxylase promoter (2007)

Sustained therapeutic effects are achieved in experimental PD with a delayed single intravenous dosing of GDNF plasmid DNA gene therapy, using receptor-targeted THLs and a region-specific promoter.
[[(Guaninylalkyl)phosphinico]methyl]phosphonic Acids. Multisubstrate Analog Inhibitors of Human Erythrocyte Purine Nucleoside Phosphorylase (1995)

A series of [[(guaninylalkyl)phosphinico]methyl]phosphonic acids, 2, was synthesized and tested as inhibitors of human erythrocyte purine nucleoside phosphorylase (PNPase). The target (phosphinicomethyl)phosphonic acids 2 were synthesized in six or seven steps from alkenylphosphonates 4. The latter were converted to the intermediate alkylmesylates 9 in a series of steps that included (1) conversion of the diethyl phosphonates 4 to the (phosphinoylmethyl)-phosphonates 7 and (2) conversion of the terminal double bond of [(alkenylphosphinoyl)methyl]-phosphonates 7 to the alkylmesylates 9. The pure 9-isomers 2 were obtained by alkylation of 2-amino-6-(2-methoxyethoxy)-9H-purine with alkylmesylates 9 followed by hydrolysis of the protecting groups with concentrated hydrochloric acid and ion exchange chromatography to give 2 as hydrated ammonium salts. The most potent inhibitor of human erythrocyte PNPase, [[[5-(2-amino-1,6-dihydro-6-oxo-9H-purin-9- yl)pentyl]phosphinico]methyl]phosphonic acid (2b), was a multisubstrate analogue inhibitor with a Ki' of 3.1 nM. Optimum PNPase inhibitory activity required the presence of zinc ions in the assay medium. These potent inhibitors of PNPase exhibited only weak activity against human leukemic T-cells in vitro.