gebhart/patrepeval huggingface dataset:
Protonated Nanoparticle Surface Governing Ligand Tethering and Cellular Targeting (2009)

Nanoparticles have shown tremendous potential for effective drug delivery due to their tiny size and cell membrane penetration capabilities. Cellular targeting with nanoparticles is often achieved by surface modifications followed by ligand conjugation. However, the efficiency of the nanoparticles reaching the target cells and getting internalized depends on the stability of targeting ligands and the chemical nature of the ligand nanoparticle binding. Recent advancements in nanobiomaterials research have proven the superoxide dismutase (SOD) mimetic activity of cerium oxide nanoparticles (CNPs) in protecting cells against oxidative stress. Due to their excellent biocompatibility, CNPs can be used as a potential drug carrier that can transport and release drugs to the malignant sites. Here we combine single molecule force spectroscopy (SMFS) and density functional theory (DFT) simulations to understand the interaction between transferrin, a ligand protein overexpressed in cancer cells, and CNPs. SMFS studies demonstrate an increase in the transferrin adhesion to the nanoparticles' surface with an increase in positive zeta potential of CNPs. Binding energy values obtained from DFT calculations predict an increase in bond strength between the transferrin and CNPs upon surface protonation and charge modification. Transferrin-conjugated CNPs were tested for their binding stability and preferential cellular uptake efficiency by incubating them with human lung cancer cells (A549) and normal embryo lung cells (WI-38). The results demonstrate the importance of tuning the surface properties of nanoparticles for better ligand adsorption and cellular uptake.
Transduction of SIV-Specific TCR Genes into Rhesus Macaque CD8+ T Cells Conveys the Ability to Suppress SIV Replication (2011)

Our results show that antigen-specific SIV suppression can be transferred between allogenic T cells simply by TCR gene transfer. This advance provides a platform for examining the contributions of TCRs versus the intrinsic effector characteristics of T-cell clones in virus suppression. Additionally, this approach can be applied to develop non-human primate models to evaluate adoptive T-cell transfer therapy for AIDS and other diseases.
Autonomic innervation of the heart. (1978)

This brief review describes recent advances in the areas of myocardial receptors that discharge into nonmyelinated, afferent, vagal C-fibers and the regional distribution of sympathetic postganglionic neurons to the myocardium. Complex, nonencapsulated nerve endings discharging into myelinated afferents have been known to exist for many years. More recently, however, indirect evidence for the existence of cardiac receptors that are either silent or exhibit low resting rates of activity, and discharge into slowly conducting C-type fibers, has been demonstrated. The receptors themselves have not yet been identified histologically. Cardiac receptors include subpopulations that are preferentially activated by chemical stimuli, including a variety of exogenous chemicals as well as prostaglandins. Another subpopulation is preferentially activated by mechanical stresses in the physiological range. Further investigation may reveal their participation in overall cardiovascular regulation, and mediation of responses to exogenous chemical stimuli. Four principal cardiac sympathetic nerves have been identified in the right thoracic region and three on the left. Most carry sympathetic and parasympathetic fibers. Stimulation of individual nerves, before and after parasympathetic blockade, results in regionally, well-defined myocardial responses.
Human monoclonal antibody identified an immunoreactive tetrapeptide sequence (Lys-Tyr-Gln-Ile) in M(r) 43,000 protein of human melanoma. (1994)

The human monoclonal antibody (HuMAb) L92 reacts to an M(r) 43,000 protein associated with human melanoma. To identify the gene encoding its antigenic epitope, a complementary DNA expression library constructed from the human melanoma cell line UCLASO M14 was screened with HuMAb L92. DNA sequence analysis of the isolated clone revealed that the immunoreactive peptide was composed of 10 amino acids (QDLT-MKYQIF). The peptide was expressed in Escherichia coli with beta-galactosidase as a fused protein. There is no homology between the cloned sequence and other reported DNA sequences. Western blot analysis showed that the fused protein had specific binding to HuMAb L92. An antigen-encoding peptide with 10 amino acids was synthesized and tested for its immunoreactivity in vitro. HuMAb L92 reacted specifically to the 10-amino acid peptide in both an antibody-binding inhibition to the M(r) 43,000 protein and a solid-phase enzyme-linked immunosorbent assay. Using several truncated fusion proteins, we found the minimum number of amino acids required for the antibody binding to be 4 (KYQI). These results suggest that the identified peptide sequence encodes the antigenic epitope of the M(r) 43,000 protein.
Fast User-Guided Video Object Segmentation by\n Interaction-and-Propagation Networks (2019)

We present a deep learning method for the interactive video object\nsegmentation. Our method is built upon two core operations, interaction and\npropagation, and each operation is conducted by Convolutional Neural Networks.\nThe two networks are connected both internally and externally so that the\nnetworks are trained jointly and interact with each other to solve the complex\nvideo object segmentation problem. We propose a new multi-round training scheme\nfor the interactive video object segmentation so that the networks can learn\nhow to understand the user's intention and update incorrect estimations during\nthe training. At the testing time, our method produces high-quality results and\nalso runs fast enough to work with users interactively. We evaluated the\nproposed method quantitatively on the interactive track benchmark at the DAVIS\nChallenge 2018. We outperformed other competing methods by a significant margin\nin both the speed and the accuracy. We also demonstrated that our method works\nwell with real user interactions.\n
Characterization of the cecal bacteria of normal pigs (1981)

One hundred ninety-two isolates from cecal contents of three normal weaned pigs were obtained by means of anaerobic roll tube methods and were characterized. Seventy-eight percent of the isolates were gram-negative. The most numerous species isolated from each of the pigs was Bacteroides ruminicola. This species accounted for 35% of the isolates that were characterized, and Selenomonas ruminantium accounted for 21% of the isolates. Other gram-negative bacteria isolated from all three pigs were Butyrivibrio fibrisolvens (6.0%) and Bacteroides uniformis (3.0%); predominant gram-positive isolates were Lactobacillus acidophilus (7.6%), Peptostreptococcus productus (3.0%), and Eubacterium aerofaciens (2.5%). The other 42 isolates were placed in 14 other species, and 5 additional isolates that did not fit well into existing species were not placed taxonomically. Fifteen of the isolates (representing nine species) produced urease.
Terminal truncations in Amp C β‐lactamase from a clinical isolate of Pseudomonas aeruginosa (1999)

AmpC beta-lactamases from strains of Pseudomonas aeruginosa have previously been shown to be heterogeneous with respect to their isoelectric point (pI). In order to elucidate the origin of this heterogeneity enzymes were isolated from a clinical isolate of a multiresistant P. aeruginosa strain and biochemically characterized. The purification was accomplished in four chromatographic steps comprising dye-affinity, size-exclusion, hydrophobic interaction chromatography, and chromatofocusing; this resulted in five forms with pI values of 9.1, 8.7, 8.3, 8.2, and 7.6. When analysed by SDS/PAGE and agarose IEF each separated beta-lactamase appeared to be both size- and charge-homogeneous. The specific activities of the variants were very similar. MS of each isolated beta-lactamase form showed minor differences in molecular mass (range 40.0-40.8 kDa). MS of the beta-lactamase with a pI of 8.2 demonstrated the presence of two subforms. The N-terminal sequences of three of the beta-lactamases were identical to the published sequence [Lodge, J.M. , Minchin, S.D., Piddock, L.J.V. & Busby, J.W. (1990) Biochem. J. 272, 627-631], while two variants were truncated by two amino-acid residues, one of which was acidic. The previously published sequence contains an alanine as the ultimate residue, but two of the beta-lactamases showed a substitution of Ala371 for arginine, whereas in the remaining forms C-terminal truncations by one and three residues were found. Our results indicate that the P. aeruginosa strain does not harbour multiple copies of the ampC gene, but rather that the five beta-lactamase isoforms are products of a single structural gene. The combinations of the identified N- and/or C-terminal truncations explained the multiple pI values of the beta-lactamase isoforms.
Future Pharmacotherapy for Non-alcoholic Steatohepatitis (NASH): Review of Phase 2 and 3 Trials (2018)

Non-alcoholic steatohepatitis (NASH) results from inflammation and hepatocyte injury in the setting of hepatic steatosis. Non-alcoholic steatohepatitis increases the risk of progression to liver fibrosis and cirrhosis, and is the most rapidly growing etiology for liver failure and indication for liver transplantation in the USA. Weight loss and lifestyle modification remain the standard first-line treatment, as no USA Food and Drug Administration-approved pharmacotherapy currently exists. The past decade has seen an explosion of interest in drug development targeting pathologic pathways in non-alcoholic steatohepatitis, with numerous phase 2 and 3 trials currently in progress. Here, we concisely review the major targets and mechanisms of action by class, summarize results from completed pivotal phase 2 studies, and provide a detailed outline of key active studies with trial data for drugs in development, including obeticholic acid, elafibranor, cenicriviroc and selonsertib.
C-Terminally Truncated Forms of Tau, But Not Full-Length Tau or Its C-Terminal Fragments, Are Released from Neurons Independently of Cell Death (2015)

Recent studies suggest that the transfer of tau between neurons underlies the characteristic spatiotemporal progression of neurofibrillary pathology. We searched for tau in the conditioned medium of N2a cells, induced pluripotent stem cell-derived human cortical neurons, and primary rat cortical neurons and analyzed the material present using four different tau ELISAs. We demonstrate that the majority of tau released from healthy neurons is C-terminally truncated and lacks the microtubule-binding region (MTBR) thought necessary for self-aggregation. A small amount of MTBR-containing tau is present outside of cells, but this appears to be solely due to cell death. Therefore, if propagation of tau aggregation is mediated by extracellular tau, our findings suggest that neuronal compromise is required to facilitate this process.
Folate Immobilized and PEGylated Adenovirus for Retargeting to Tumor Cells (2006)

The surface of adenovirus (ADV) was modified with folate-poly(ethylene glycol) (FOL-PEG) conjugate to overcome the inherent problems associated with viral gene therapy. The ADV coding the green fluorescent protein (GFP) gene was used to immobilize PEG or FOL-PEG conjugate on the viral surface to comparatively evaluate their extents of retargeting and immune response, as compared to those of naked ADV. The FOL-PEG immobilized ADV exhibited a greatly enhanced level of GFP expression than naked or PEG immobilized ADV for a folate receptor overexpressing cell line (KB cells), but not for a folate receptor deficient cell line (A549 cells), suggesting that the retargeting of ADV could be achieved by immobilizing FOL-PEG conjugate. The ADV immobilized with PEG or FOL-PEG also significantly lowered innate immune response, as judged from the amount of interleukin 6 released from macrophage cells.
Promoter analysis of genes that are coordinately expressed during pollen development reveals pollen-specific enhancer sequences and shared regulatory elements. (1991)

We have investigated the functional organization and properties of cis regulatory elements in the promoter regions of two genes from tomato (LAT52 and LAT59) that are preferentially and coordinately expressed during pollen maturation. Promoter deletion analysis in transgenic plants demonstrated that only minimal (less than 200 bp) promoter proximal regions are required for developmentally regulated expression in pollen and in specific cell types of the sporophyte. Cis-acting regulatory regions of these two promoters and of a third pollen-expressed promoter (LAT56) were characterized in detail using a transient expression assay. We identified two upstream activator regions in the LAT52 promoter and further showed that a 19-bp segment from one of those regions enhanced expression of the heterologous CaMV35S promoter in pollen. Similarities in sequence between crucial cis elements provide evidence that shared regulatory elements are involved in the coordinate expression of the LAT genes during microsporogenesis.
Conductance and kinetics of delayed rectifier potassium channels in nodal cells of the rabbit heart. (1987)

1. The delayed rectifier K+ current (IK) of single pace‐maker cells from the sino‐atrial node and the atrioventricular node of the rabbit heart was investigated using the whole‐cell and cell‐attached configurations of the patch‐clamp technique. 2. The activation kinetics of the macroscopic IK were not altered by varying the extracellular K+ concentration ([K+]o) between 5.4 and 150 mM. The amplitude of the tail current of IK, however, was about 10‐fold larger at a [K+]o of 150 mM than that at a [K+]o of 5.4 mM. 3. By using a high‐[K+]o solution, inward single‐channel currents were observed on repolarization from potentials positive to ‐40 mV. The current‐voltage (I‐V) relation was linear over the negative potential range and the reversal potential estimated by extrapolating the I‐V curve was shifted by about 60 mV for a 10‐fold increase in [K+]o, indicating that the channel was highly selective for K+. 4. The single‐channel conductance was 11.1 pS at a [K+]o of 150 mM and varied in proportion to the square root of [K+]o. The total number of channels was estimated as approximately 1000 per cell (0.7/micron 2). On repolarization, the averaged single‐channel current disappeared with a time constant similar to that of the macroscopic tail current of IK. 5. At potentials between ‐50 and ‐100 mV, the open and closed times of the single channel fitted well with single‐exponential and biexponential distributions, respectively. As the membrane was progressively depolarized, the open time was shortened while the closed time was prolonged, suggesting a decrease of open probability. These changes were in the opposite direction to those expected from the delayed rectifier K+ current which progressively increases in magnitude at more positive potentials. 6. At the beginning of the macroscopic tail current, a transient increase of the inward current was found to precede the time‐dependent decrease. This rapid initial change can be attributed to a quick removal of inactivation of IK which had occurred during the depolarizing pulse. This inactivation gate of the channel has very fast kinetics and could be responsible for the inward‐going rectification observed in the 'fully activated' IK.
Searching for candidate genes in the new millennium (2001)

Completion of the entire sequence of the human genome is having a profound effect on the strategies biological scientists use to identify disease-associated genes. Laborious positional cloning approaches and traditional functional studies are gradually being transformed by emerging genomic and proteomic databases. Some of the exciting challenges investigators now face are the identification of new genes, determining the function of these genes, defining disease associations, and elucidating correlation between genotype and phenotype. To demonstrate how investigative methods for single-gene disorders are changing, we illustrate one possible approach in the search for the gene underlying the autosomal recessive genodermatosis, acrodermatitis enteropathica.
Localization of muscarinic receptor mRNAs in rat heart and intrinsic cardiac ganglia by in situ hybridization. (1994)

Although the heart is considered a relatively pure source of m2 muscarinic receptors, the possible expression of other muscarinic receptor genes at discrete sites within the myocardium or by intrinsic cardiac ganglia had not been evaluated. Accordingly, the present study used in situ hybridization histochemistry with 35S-labeled oligonucleotide probes to address this issue. Initial experiments demonstrated that the localization of m2 mRNA was similar to that reported for muscarinic receptors labeled with the nonselective muscarinic antagonist quinuclidinyl benzilate; however, there were two important exceptions. The conducting system contained less message than expected, whereas the intrinsic cardiac ganglia contained more. The mismatch between muscarinic receptor and m2 mRNA densities in the conducting system could not be explained by the local expression of other muscarinic receptor genes, since m1, m3, and m4 mRNAs were not detected at this or any other site within the myocardium. However, the presence of a high density of prejunctional muscarinic receptors in the conducting system would be consistent with such a mismatch. Surprisingly, the intrinsic cardiac ganglia contained more than four times as much m2 mRNA as found in the atria. This level of message may be necessary for the production of prejunctional receptors on cholinergic nerve fibers within the heart and receptors localized to the ganglion cell bodies. The ganglia also contained smaller amounts of m1 and m4 mRNAs. These observations suggest that prejunctional muscarinic receptors could have a prominent role in regulating cholinergic neurotransmission in the conducting system and that multiple muscarinic receptors are present in the intrinsic cardiac ganglia.
The Neurology of Cobalamin (1992)

The following review indicates that the impact of cobalamin on neurologic disease extends far beyond the traditional myelopathy of classical pernicious anemia. The delineation of a broad spectrum of inherited disorders of cobalamin processing has served to illustrate and precisely define each step in the normal absorption, transport and intracellular metabolism of this essential vitamin. Recent clinical work has extended the boundaries of acquired cobalamin deficiency to encompass a variety of neuropsychiatric disturbances without identifiable concomitant hematologic derangements and emphasized the utility and sensitivity of new laboratory tests. These findings will demand increased vigilance from clinicians so that atypical and subtle cobalamin deficiency states will be readily diagnosed. The wide range of neurologic dysfunction observed in both inherited and acquired disorders of cobalamin metabolism challenges basic scientists to delineate cobalamin's presumed important role in the normal development and homeostasis of the nervous system.
Characterization of digital recording channels by means of echo cancellation techniques (1989)

A simple yet accurate method is described for characterizing digital recording channels in terms of linear and nonlinear intersymbol interference and noise. The method is based on echo cancellation techniques, enables recorder operating conditions close to actual use, and delivers a joint portrait of the disturbances rather than isolated assessments. Experimental results for a high-density digital video tape recorder are included.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Intracellular Interleukin-1α Production in Human Gingival Fibroblasts is Differentially Regulated by Various Cytokines (1999)

Interleukin-1 (IL-1) may play a critical role in immune and inflammatory responses in inflamed gingiva, and it is synthesized by a wide variety of host cells. In this study, we examined the regulatory effects of various cytokines on bioactive membrane IL-1 and intracellular IL-1 alpha production in cultured human gingival fibroblasts (HGF). Recombinant human (rh) IL-1 beta stimulated membrane IL-1 activity, which was mainly attributed to IL-1 alpha. rhIL-1 beta and rh tumor necrosis factor (TNF)-alpha stimulated HGF to produce intracellular IL-1 alpha, whereas rh interleukin-6 (IL-6), rh interleukin-4 (IL-4), and rh interferon (IFN)-gamma did not do so. Intracellular IL-1 alpha production induced by rhIL-1 beta or rhTNF-alpha may be partially related to protein kinase C (PKC) activation, because rhIL-1 beta or rhTNF-alpha-induced intracellular IL-1 alpha production was stimulated by pre-treatment with 12-o-tetradecanoylphorbol 13-acetate (TPA), a PKC activator, but was suppressed by the pre-treatment with 1-(5-isoquinoline-sulfonyl) -2-methylpiperazine dihydrochloride (H-7), which is a PKC inhibitor. rhIL-4 inhibited rhIL-1 beta- or rhTNF-alpha-induced intracellular IL-1 alpha production, but rhIL-6 had no effect on this production. Pre-treatment with rh IFN-gamma remarkably enhanced intracellular IL-1 alpha production induced by subsequent treatment with rhIL-1 beta or rhTNF-alpha. Simultaneous treatment with rhIFN-gamma and rhIL-1 beta inhibited rhIL-1 beta-induced intracellular IL-1 alpha production, but co-treatment with rhIFN-gamma and rhTNF-alpha enhanced rhTNF-alpha-induced intracellular IL-1 alpha production. These results suggest that in inflamed gingiva, pro-inflammatory cytokines such as IL-1 beta and TNF-alpha may induce bioactive intracellular IL-1 alpha production in human gingival fibroblasts and that this production can be differentially modulated by T-cell-derived cytokines such as IFN-gamma or IL4.
Not All Sequence Tags Are Created Equal: Designing and Validating Sequence Identification Tags Robust to Indels (2012)

Ligating adapters with unique synthetic oligonucleotide sequences (sequence tags) onto individual DNA samples before massively parallel sequencing is a popular and efficient way to obtain sequence data from many individual samples. Tag sequences should be numerous and sufficiently different to ensure sequencing, replication, and oligonucleotide synthesis errors do not cause tags to be unrecoverable or confused. However, many design approaches only protect against substitution errors during sequencing and extant tag sets contain too few tag sequences. We developed an open-source software package to validate sequence tags for conformance to two distance metrics and design sequence tags robust to indel and substitution errors. We use this software package to evaluate several commercial and non-commercial sequence tag sets, design several large sets (max(count) = 7,198) of edit metric sequence tags having different lengths and degrees of error correction, and integrate a subset of these edit metric tags to polymerase chain reaction (PCR) primers and sequencing adapters. We validate a subset of these edit metric tagged PCR primers and sequencing adapters by sequencing on several platforms and subsequent comparison to commercially available alternatives. We find that several commonly used sets of sequence tags or design methodologies used to produce sequence tags do not meet the minimum expectations of their underlying distance metric, and we find that PCR primers and sequencing adapters incorporating edit metric sequence tags designed by our software package perform as well as their commercial counterparts. We suggest that researchers evaluate sequence tags prior to use or evaluate tags that they have been using. The sequence tag sets we design improve on extant sets because they are large, valid across the set, and robust to the suite of substitution, insertion, and deletion errors affecting massively parallel sequencing workflows on all currently used platforms.