gebhart/patrepeval huggingface dataset:
Membrane Type 1-Matrix Metalloproteinase Is Activated during Migration of Human Endothelial Cells and Modulates Endothelial Motility and Matrix Remodeling (2001)

Matrix metalloproteinases are thought to play an important role in endothelial cell migration and matrix remodeling. We have used an in vitro wound healing migration model and newly generated anti-membrane type 1-matrix metalloproteinase (MT1-MMP) monoclonal antibodies (mAbs) to characterize the role of MT1-MMP during this process. First, the expression and shedding of MT1-MMP are up-regulated upon induction of migration in endothelial cells, as demonstrated by flow cytometry and Western blot analysis. Furthermore, MT1-MMP is concentrated at discrete areas in migrating endothelial cells, in contrast to the diffuse pattern observed in confluent cells. Interestingly, migration of endothelial cells results in the stimulation of MT1-MMP activity, as shown by its ability to process pro-MMP-2 and to degrade fibrinogen assessed by zymography. Moreover, MT1-MMP-mediated gelatin degradation is enriched at migration sites. mAbs generated against the MT1-MMP catalytic domain are shown to inhibit MT1-MMP enzymatic activity and to impair both phorbol 12-myristate 13-acetate-induced endothelial migration and invasion of collagen and fibrin gels. Furthermore, a reduction in the formation of capillary tubes in Matrigel is also observed when endothelial cells are pretreated with the blocking anti-MT1-MMP mAbs. Altogether, these data demonstrate that MT1-MMP plays an important role during endothelial cell migration, and its activity can modulate endothelial migration, invasion, and formation of capillary tubes during the angiogenic response.
Cloning and Characterization of the Hakata Antigen, a Member of the Ficolin/Opsonin p35 Lectin Family (1998)

The Hakata antigen is a novel, thermolabile beta2-macroglycoprotein that reacts with sera from patients suffering from systemic lupus erythematosus. In this study we present the structure and the function of the Hakata antigen. We have identified cDNA clones encoding the Hakata antigen and analyzed its function. The cDNA included a possible open reading frame of 897 nucleotides, encoding 299 amino acids. The Hakata antigen consisted of a collagen-like domain in the middle section and a fibrinogen-like domain in the COOH terminus, both of which are homologous to human ficolin-1 and opsonin P35, indicating that these three molecules form a distinct family. The molecular mass of the Hakata antigen expressed in transfected cells was 35 kDa under reduced conditions, and it formed ladder bands under nonreducing conditions compatible with the previous result that the Hakata antigen exists in serum as homopolymers. Purified Hakata antigen sustained lectin activity, showing affinity with GalNAc, GlcNAc, D-fucose as mono/oligosaccharide, and lipopolysaccharides from Salmonella typhimurium and Salmonella minnesota. These results suggest that the Hakata antigen, a new member of the ficolin/opsonin P35 family, plays a role in the serum exerting lectin activity under physiological conditions.
CORTICAL AND SUBCORTICAL ARGYROPHILIC GRAINS CHARACTERIZE A DISEASE ASSOCIATED WITH ADULT ONSET DEMENTIA (1989)

Unusual cytoskeleton abnormalities were found in the brains of 28 individuals afflicted with adult onset dementia. Most conspicuous were small spindle-shaped argyrophilic grains loosely scattered throughout the neuropil. Additionally, coiled bodies of silver-stained filaments were encountered, mainly located within the white matter close to the cortical grey matter. Argyrophilic grains and coiled bodies contained dense accumulations of straight filaments with a diameter of about 9 nm. The argyrophilic grains were found in abundance within sector CA1 of the Ammon's horn and layer Pre-beta of the entorhinal region. A slightly less dense scattering of the grains occurred in layer IIIab of the adjoining temporal isocortex, insular cortex and orbitofrontal cortex. The basolateral amygdaloid complex and the hypothalamic lateral tuberal nucleus were the most affected subcortical structures. Deeper brain stem nuclei merely showed a sparse number of grains or were devoid of them. Eighty brains of demented individuals were examined. Forty-eight of them showed the features of Alzheimer's disease and four showed the features of Pick's disease. Twenty-eight cases revealed the abnormalities under consideration. Ten showed exclusively argyrophilic grains and coiled bodies, while 16 also had neuritic plaques, neurofibrillary tangles, and neuropil threads. One of the 28 cases was associated with Parkinson's disease and one showed features of both Parkinson's and Alzheimer's disease. Twenty brains of non-demented individuals of about the same age and devoid or almost devoid of Alzheimer changes were used as controls. None of the control brains showed the presence of argyrophilic grains and coiled bodies. These changes, therefore, are considered the morphological substrate of an unknown disease associated with adult onset dementia.
Unmasking cryptic epitopes after loss of immunodominant tumor antigen expression through epitope spreading (2001)

The basis of intra-tumoral and systemic T cell reactivity toward cancer remains unclear. In particular the role that peripheral stimuli, whether endogenous or exogenous, play in shaping acquired immune response toward cancer remains poorly understood. In this study we document the surfacing of systemic immune reactivity toward a cryptic epitope from the MAGE-12 gene (MAGE-12:170-178), after temporary regression of a single melanoma metastasis, in response to gp100/PMel17-specific vaccination. This emergence was unlikely related to unusually high expression of MAGE-12 by the tumor, by the influence of analog epitopes to MAGE-12:170-178. Because MAGE-12 was unlikely to be expressed at sites other than the tumor, the demonstration of MAGE-12:170-178 reactivity in post- but not pre-vaccination circulating lymphocytes suggests that the systemically observed immune response was influenced by events induced by the vaccine at tumor site or draining lymph nodal areas. Possibly, as suggested by pre-clinical models, immunologic ignorance is the default response toward cancer in humans unless unusual stimulatory conditions occur in peripheral tissues. Surfacing of MAGE-12 specificity occurred in association with loss of gp100/PMel 17 targeted by the vaccine. This finding suggests that vaccinations might have effects beyond their intrinsic specificity and may trigger broader immune responses through epitope spreading by inducing changes within the tumor microenvironment. This may have important practical implication for the development of immunization strategies. Published 2001 Wiley-Liss, Inc.
Use of Electrical Stimulation at Different Current Levels to Promote Recovery After Peripheral Nerve Injury in Rats (2009)

Indeed, the electrical stimulation appears to have a detrimental effect on the regeneration process. It could promote the growth of regenerating nerves; however, excessive direct current could be repulsive to regrowing fibers. This reveals the importance for physical therapists using safe stimulus protocols for rehabilitation purposes.
Quinoxaline-Based Polymer Dots with Ultrabright Red to Near-Infrared Fluorescence for In Vivo Biological Imaging (2015)

This article describes the design and synthesis of quinoxaline-based semiconducting polymer dots (Pdots) that exhibit near-infrared fluorescence, ultrahigh brightness, large Stokes shifts, and excellent cellular targeting capability. We also introduced fluorine atoms and long alkyl chains into polymer backbones and systematically investigated their effect on the fluorescence quantum yields of Pdots. These new series of quinoxaline-based Pdots have a fluorescence quantum yield as high as 47% with a Stokes shift larger than 150 nm. Single-particle analysis reveals that the average per-particle brightness of the Pdots is at least 6 times higher than that of the commercially available quantum dots. We further demonstrated the use of this new class of quinoxaline-based Pdots for effective and specific cellular and subcellular labeling without any noticeable nonspecific binding. Moreover, the cytotoxicity of Pdots were evaluated on HeLa cells and zebrafish embryos to demonstrate their great biocompatibility. By taking advantage of their extreme brightness and minimal cytotoxicity, we performed, for the first time, in vivo microangiography imaging on living zebrafish embryos using Pdots. These quinoxaline-based NIR-fluorescent Pdots are anticipated to find broad use in a variety of in vitro and in vivo biological research.
IS NOMA NEONATORUM A PRESENTATION OF ECTHYMA GANGRENOSUM IN THE NEWBORN? (2002)

Noma neonatorum was suggested as a distinct entity characterized by a gangrenous process of the nose, oral cavity, eyelids and perineum that was almost universally fatal in premature infants with Pseudomonas sepsis. We report the first case of noma neonatorum in a 26-week-gestation twin born in the United States. Our case is consistent with previous descriptions of noma neonatorum; however, we question the distinction between noma neonatorum and a neonatal presentation of ecthyma gangrenosum.
Synthesis of Facial Amphiphile 3,7-Diamino-5α-cholestane Derivatives as a Molecular Receptor (2009)

A series of facial amphiphiles 3,7-diaminocholestane were synthesized from 3,7-diketocholestane via 2 sequential reductive aminations and anion recognition was evaluated with acetate, chloride, bromide, fluoride and phosphate anions. The stereo-selective reductive amination protocol was utilized to synthesized facial amphiphiles afforded receptors in high yields. The molecular receptor 2 showed the highest binding constant with acetate in a 1:1 ratio.
Overexpression of Mitochondrial Hsp70/Hsp75 in Rat Brain Protects Mitochondria, Reduces Oxidative Stress, and Protects from Focal Ischemia (2008)

Mitochondria are known to be central to the cell's response to ischemia, because of their role in energy generation, in free radical generation, and in the regulation of apoptosis. Heat shock protein 75 (Hsp75/Grp75/mortalin/TRAP1) is a member of the HSP70 chaperone family, which is targeted to mitochondria. Overexpression of Hsp75 was achieved in rat brain by DNA transfection, and expression was observed in both astrocytes and neurons. Rats were subjected to 100 mins middle cerebral artery occlusion followed by assessment of infarct volume, neurological score, mitochondrial function, and levels of oxidative stress at 24 h reperfusion. Overexpression of Hsp75 reduced infarct area from 44.6%+/-21.1% to 25.7%+/-12.1% and improved neurological outcome significantly. This was associated with improved mitochondrial function as shown by protection of complex IV activity, marked reduction of free radical generation detected by hydroethidine fluorescence, reduction of lipid peroxidation detected by 4-hydroxy-2-nonenol immunoreactivity, and increased preservation of ATP levels. This suggests that targeting mitochondria for protection may be a useful strategy to reduce ischemic brain injury.
Redox State of the Endoplasmic Reticulum Is Controlled by Ero 1L-alpha and Intraluminal Calcium (2010)

Formation of intra- and intermolecular disulfide bonds is an essential step in the synthesis of secretory proteins. In eukaryotic cells, this process occurs in the endoplasmic reticulum (ER) and requires an oxidative environment with the action of several chaperones and folding catalysts. During protein folding, Ero1p oxidizes protein disulfide isomerase (PDI), which then directly catalyzes the formation of disulfide bonds in folding proteins. Recent cell-free studies suggest that the terminal electron acceptor in the pathway is molecular oxygen, with the resulting formation of hydrogen peroxide (H(2)O(2)). We report for the first time the measurement of ER H(2)O(2) level in live cells. By targeting a fluorescent protein-based H(2)O(2) sensor to various intracellular compartments, we show that the ER has the highest level of H(2)O(2), and this high concentration is well confined to the lumen of the organelle. Manipulation of the Ero1-Lalpha level--either by overexpression or by siRNA-mediated inhibition--caused parallel changes in luminal H(2)O(2), proving that the activity of Ero1-Lalpha results in H(2)O(2) formation in the ER. We also found that calcium mobilization from intracellular stores induces a decrease in ER H(2)O(2) level, suggesting a complex interplay between redox and calcium signaling in the mammalian ER.
Sinusoidal modeling and modification of unvoiced speech (1997)

Although sinusoidal models have been shown to be useful for time-scale and pitch modification of voiced speech, objectionable artifacts often arise when such models are applied to unvoiced speech. This article presents a sinusoidal model-based speech modification algorithm that preserves the natural character of unvoiced speech sounds after pitch and time-scale modification, eliminating commonly encountered artifacts. This advance is accomplished via a perceptually motivated modulation of the sinusoidal component phases that mitigates artifacts in the reconstructed signal after time-scale and pitch modification.
The expression of normal ventricular repolarization in the body surface distribution of T potentials. (1976)

Isopotential maps from 120 normal subjects were obtained from 192 simultaneously recorded electrocardiographic leads. Maps were plotted at 1 msec intervals during the QRS and 5 msec intervals during the ST-T deflection. Repetition of QRS features was evident during all but the first few msec of the initial half of serial T maps. This suggests similarities of the normal sequence of ventricular excitation and recovery. Such similarities have been demonstrated by direct studies but are not evident from other electrocardiographic examinations. Serial maps during later portions of the T wave showed decreasing intensity of potentials with little change of body surface locations. This also correlates with an established feature of ventricular repolarization, namely that potential difference boundaries with stable locations are widely distributed during part of that process. Findings suggest isopotential maps show features of ventricular recovery not apparent from less extensive examinations.
Influence of Within-Orchard Trap Placement on Catch of Codling Moth (Lepidoptera: Tortricidae) in Sex Pheromone–Treated Orchards (2007)

The influence of trap placement on catches of codling moth, Cydia pomonella L., was examined in a series of studies conducted in orchards treated with Isomate-C Plus sex pheromone dispensers. Mark-recapture tests with sterilized moths released along the interface of pairs of treated and untreated apple and pear plots found that significantly more male but not female moths were recaptured on interception traps placed in the treated plots. In a second test, significantly higher numbers of wild male and female moths were caught on interception traps placed in treated versus untreated plots within a heavily infested orchard. The highest numbers of male moths were caught on traps placed along the interior edge of the treated plots. Trap position had no influence on the captures of female moths. In a third test, north-south transects of sex pheromone-baited traps were placed through adjacent treated and untreated plots that received a uniform release of sterilized moths. Traps on the upwind edge of the treated plots caught similar numbers of moths as traps upwind from the treated plots. Moth catch was significantly reduced at all other locations inside versus outside of the treated plots, including traps placed on the downwind edge of the treated plot. In a fourth test, five apple orchards were monitored with groups of sex pheromone-baited traps placed either on the border or at three distances inside the orchards. The highest moth counts were in traps placed at the border, and the lowest moth counts were in traps placed 30 and 50 m from the border. In a fifth test, the proportion of traps failing to catch any moths despite the occurrence of local fruit injury was significantly higher in traps placed 50 versus 25 m from the border. The implications provided by these data for designing an effective monitoring program for codling moth in sex pheromone-treated orchards are discussed.
Nonselective Bromination−Selective Debromination Strategy:  Selective Bromination of Unsymmetrical Ketones on Singly Activated Carbon against Doubly Activated Carbon (2003)

[reaction: see text] We have found a new synthetic method for the preparation of the alpha-bromoketones that are brominated in the less activated terminal position of unsymmetrical ketones. Brominations in short reaction times (kinetically controlled) provided internally brominated compounds as a major product. However, brominations in longer reaction times (thermodynamically controlled) gave more of the terminally brominated compound through the reversible reaction by Br(2) and produced hydrogen bromide. Several brominated compounds at the terminal position were successfully prepared through the new synthetic route.
Mapping of DNA Alkylation Sites Induced by Adozelesin and Bizelesin in Human Cells by Ligation-Mediated Polymerase Chain Reaction (1994)

In this study, we have mapped the intracellular alkylation sites of adozelesin and bizelesin, two potent analogs of CC-1065, in individual genes at the single-nucleotide level. Human colon carcinoma cells were treated with adozelesin and bizelesin, and the position of adducts were mapped within the PGK-1 and p53 genes by means of ligation-mediated polymerase chain reaction. The monofunctional alkylating agent adozelesin was found to alkylate genomic DNA predominantly within 5'-(A/T)(A/T)A* sequences. Additional sites of alkylation were observed within 5'-(A/T)(G/C)(A/T)A* sequences; however, these were considered to represent sites of medium to low preference. Bizelesin, a bifunctional analog capable of both DNA monofunctional alkylation and DNA interstrand cross-link formation, was also found to alkylate 5'-(A/T)(A/T)A* sequences. Putative bizelesin DNA interstrand cross-link sites indicated that AT-rich sequences are preferred in the intervening sequence between the two cross-linked adenines. Both six- and seven-nucleotide regions were identified as putative sites of DNA interstrand cross-link formation with 5'-TTTTTTA*, 5'-TTTATCA* and 5'-GTACTAA* sequences being preferred. Non-adenine bases are not observed as potential intracellular sites of either DNA interstrand cross-linking formation or monofunctional alkylation. Thus, the patterns of alkylation induced by adozelesin and bizelesin in genomic DNA are similar but not identical to that observed in purified cell-free DNA.
Signal pathway profiling of prostate cancer using reverse phase protein arrays (2003)

Reverse phase protein arrays represent a new proteomics microarray technology with which to study the fluctuating state of the proteome in minute quantities of cells. The activation status of cell signaling pathways controls cellular fate and deregulation of these pathways underpins carcinogenesis. Changes in pathway activation that occur between early stage prostatic epithelial lesions, prostatic stroma and the extracellular matrix can be analyzed by obtaining pure populations of cell types by laser capture microdissection (LCM) and analyzing the relative states of several key phosphorylation points within the cellular circuitry. We have applied reverse phase protein array technology to analyze the status of key points in cell signaling involved in pro-survival, mitogenic, apoptotic and growth regulation pathways in the progression from normal prostate epithelium to invasive prostate cancer. Using multiplexed reverse phase protein arrays coupled with LCM, the states of signaling changes during disease progression from prostate cancer study sets were analyzed. Focused analysis of phospho-specific endpoints revealed changes in cellular signaling events through disease progression and between patients. We have used a new protein array technology to study specific molecular pathways believed to be important in cell survival and progression from normal epithelium to invasive carcinoma directly from human tissue specimens. With the advent of molecular targeted therapeutics, the identification, characterization and monitoring of the signaling events within actual human biopsies will be critical for patient-tailored therapy.
Synthesis of Cu2O Nanocrystals from Cubic to Rhombic Dodecahedral Structures and Their Comparative Photocatalytic Activity (2011)

In this study, a new series of Cu(2)O nanocrystals with systematic shape evolution from cubic to face-raised cubic, edge- and corner-truncated octahedral, all-corner-truncated rhombic dodecahedral, {100}-truncated rhombic dodecahedral, and rhombic dodecahedral structures have been synthesized. The average sizes for the cubes, edge- and corner-truncated octahedra, {100}-truncated rhombic dodecahedra, and rhombic dodecahedra are approximately 200, 140, 270, and 290 nm, respectively. An aqueous mixture of CuCl(2), sodium dodecyl sulfate, NaOH, and NH(2)OH·HCl was prepared to produce these nanocrystals at room temperature. Simple adjustment of the amounts of NH(2)OH·HCl introduced enables this particle shape evolution. These novel particle morphologies have been carefully analyzed by transmission electron microscopy (TEM). The solution color changes quickly from blue to green, yellow, and then orange within 1 min of reaction in the formation of nanocubes, while such color change takes 10-20 min in the growth of rhombic dodecahedra. TEM examination confirmed the rapid production of nanocubes and a substantially slower growth rate for the rhombic dodecahedra. The rhombic dodecahedra exposing only the {110} facets exhibit an exceptionally good photocatalytic activity toward the fast and complete photodegradation of methyl orange due to a high number density of surface copper atoms, demonstrating the importance of their successful preparation. They may serve as effective and cheap catalysts for other photocatalytic reactions and organic coupling reactions.
Design, Synthesis, and Characterization of pH-Sensitive PEG−PE Conjugates for Stimuli-Sensitive Pharmaceutical Nanocarriers:  The Effect of Substitutes at the Hydrazone Linkage on the pH Stability of PEG−PE Conjugates (2007)

A set of aliphatic and aromatic aldehyde-derived hydrazone (HZ)-based acid-sensitive polyethylene glycol-phosphatidylethanolamine (PEG-PE) conjugates was synthesized and evaluated for their hydrolytic stability at neutral and slightly acidic pH values. The micelles formed by aliphatic aldehyde-based PEG-HZ-PE conjugates were found to be highly sensitive to mildly acidic pH and reasonably stable at physiologic pH, while those derived from aromatic aldehydes were highly stable at both pH values. The pH-sensitive PEG-PE conjugates with controlled pH sensitivity may find applications in biological stimuli-mediated drug targeting for building pharmaceutical nanocarriers capable of specific release of their cargo at certain pathological sites in the body (tumors, infarcts) or intracellular compartments (endosomes, cytoplasm) demonstrating decreased pH.