gebhart/patrepeval huggingface dataset:
Thermosensitive liposomes entrapping iron oxide nanoparticles for controllable drug release (2009)

Iron oxide nanoparticles can serve as a heating source upon alternative magnetic field (AMF) exposure. Iron oxide nanoparticles can be mixed with thermosensitive nanovehicles for hyperthermia-induced drug release, yet such a design and mechanism may not be suitable for controllable drug release applications in which the tissues are susceptible to environmental temperature change such as brain tissue. In the present study, iron oxide nanoparticles were entrapped inside of thermosensitive liposomes for AMF-induced drug release while the environmental temperature was maintained at a constant level. Carboxyfluorescein was co-entrapped with the iron oxide nanoparticles in the liposomes as a model compound for monitoring drug release and environmental temperature was maintained with a water circulator jacket. These experiments have been successfully performed in solution, in phantom and in anesthetized animals. Furthermore, the thermosensitive liposomes were administered into rat forearm skeletal muscle, and the release of carboxylfluorescein triggered by the external alternative magnetic field was monitored by an implanted microdialysis perfusion probe with an on-line laser-induced fluorescence detector. In the future such a device could be applied to simultaneous magnetic resonance imaging and non-invasive drug release in temperature-sensitive applications.
Vascular endothelial growth factor and endometriotic angiogenesis (2000)

Peritoneal endometriosis is a significant debilitating gynaecological problem of widespread prevalence. It is now generally accepted that the pathogenesis of peritoneal endometriosis involves the implantation of exfoliated endometrium. Essential for its survival is the generation and maintenance of an extensive blood supply both within and surrounding the ectopic tissue. The vascular endothelial growth factor (VEGF) family of angiogenic molecules is involved in both physiological angiogenesis, and a number of pathological conditions that are characterized by excessive angiogenesis. Increasing evidence suggests that the VEGF family may also be involved with both the aetiology and maintenance of peritoneal endometriosis. Sources of this factor include the eutopic endometrium, ectopic endometriotic tissue and peritoneal fluid macrophages. Important to its aetiology is the correct peritoneal environment in which the exfoliated endometrium is seeded and implants. Established ectopic tissue is then dependent on the peritoneal environment for its survival, an environment that supports angiogenesis. Our increasing knowledge of the involvement of the VEGF family in endometriotic angiogenesis raises the possibility of novel approaches to its medical management, with particular focus on the anti-angiogenic control of the action of VEGF.
High-temperature annealing and optical activation of Eu-implanted GaN (2004)

Europium was implanted into GaN through a 10nm thick epitaxially grown AlN layer that protects the GaN surface during the implantation and also serves as a capping layer during the subsequent furnace annealing. Employing this AlN layer prevents the formation of an amorphous surface layer during the implantation. Furthermore, no dissociation of the crystal was observed by Rutherford backscattering and channeling measurements for annealing temperatures up to 1300°C. Remarkably, the intensity of the Eu related luminescence, as measured by cathodoluminescence at room temperature, increases by one order of magnitude within the studied annealing range between 1100 and 1300°C.
The Role of Venlafaxine in the Treatment of Obsessive—Compulsive Disorder (2004)

Although the relative scarcity of data precludes definitive conclusions, available evidence suggests that venlafaxine is effective and well tolerated in the treatment of OCD. Unfortunately, it has not shown any unique advantages relative to currently available medications.
Self-Assembling Cyclic β3-Peptide Nanotubes as Artificial Transmembrane Ion Channels (1998)

A new class of self-assembling transmembrane ion channels based on cyclic β3-peptides is described. Cyclic peptide subunits were designed to adopt flat, ring shaped conformations and stack through extensive backbone-backbone hydrogen bonding to form tubular channel structures. Candidate channel-forming peptides cyclo[(-β3-HTrp)4-] 1, cyclo[(-β3-HTrp-β-HLeu)2-] 2, and cyclo[(-β3-HLeu)4-] 3 were examined in liposome-based proton transport assays and single channel conductance experiments. Compounds 1 and 2 exhibited remarkable ion transport activities with single-channel K+ conductance of 56 pS for peptide 1, while compound 3 was inactive, possibly due to its poor solubility. Additionally, the putative structure of transmembrane channels formed by peptides 1 and 2 was supported by FT-IR spectroscopy of membrane-peptide preparations. The present system not only complements that of channel-forming cyclic d,l-α-peptides previously reported from this laboratory but also is expected to exhibit novel properties arising from the unnatural β3-peptide backbone.
The Ubiquitin-Proteasome Proteolytic Pathway: Destruction for the Sake of Construction (2002)

Between the 1960s and 1980s, most life scientists focused their attention on studies of nucleic acids and the translation of the coded information. Protein degradation was a neglected area, considered to be a nonspecific, dead-end process. Although it was known that proteins do turn over, the large extent and high specificity of the process, whereby distinct proteins have half-lives that range from a few minutes to several days, was not appreciated. The discovery of the lysosome by Christian de Duve did not significantly change this view, because it became clear that this organelle is involved mostly in the degradation of extracellular proteins, and their proteases cannot be substrate specific. The discovery of the complex cascade of the ubiquitin pathway revolutionized the field. It is clear now that degradation of cellular proteins is a highly complex, temporally controlled, and tightly regulated process that plays major roles in a variety of basic pathways during cell life and death as well as in health and disease. With the multitude of substrates targeted and the myriad processes involved, it is not surprising that aberrations in the pathway are implicated in the pathogenesis of many diseases, certain malignancies, and neurodegeneration among them. Degradation of a protein via the ubiquitin/proteasome pathway involves two successive steps: 1) conjugation of multiple ubiquitin moieties to the substrate and 2) degradation of the tagged protein by the downstream 26S proteasome complex. Despite intensive research, the unknown still exceeds what we currently know on intracellular protein degradation, and major key questions have remained unsolved. Among these are the modes of specific and timed recognition for the degradation of the many substrates and the mechanisms that underlie aberrations in the system that lead to pathogenesis of diseases.
Alternative Translation Initiation of the Moloney Murine Leukemia Virus mRNA Controlled by Internal Ribosome Entry Involving the p57/PTB Splicing Factor (1995)

Moloney murine leukemia virus (Mo-MuLV) genomic mRNA codes for two gag precursors by alternative initiations of translation. An AUG codon governs the synthesis of the retroviral capsid proteins precursor, whereas a CUG codon directs the synthesis of a glycosylated cell surface antigen, the gross cell surface antigen. Control of the relative synthesis of the two precursors is crucial for MuLV infectivity and pathology. Furthermore, the MuLV mRNA leader sequence is very long and should inhibit translation according to the classical scanning model. This suggests a different translation initiation mechanism allowing gag efficient expression. We demonstrate, by using bicistronic vectors expressed in COS-7 cells, that the Mo-MuLV mRNA leader drives translation initiation by internal ribosome entry. We have localized the internal ribosome entry site (IRES) between the two initiation codons. This 126 nucleotide long IRES implies an oligopyrimidine tract located 45 nucleotides upstream of AUG codon. UV cross-linking and affinity chromatography experiments show that the PTB/p57 splicing factor specifically interacts with this oligopyrimidine tract. The MuLV IRES controls alternative translation initiation by activating the capsid protein precursor expression. This gag translational enhancer could exist in other retroviruses.
Exaggerated Spontaneous Release of Platelet-Derived Growth Factor by Alveolar Macrophages from Patients with Idiopathic Pulmonary Fibrosis (1987)

Idiopathic pulmonary fibrosis is a fibrotic lung disease characterized by an increased number of mesenchymal cells in the alveolar walls. Alveolar macrophages constitutively express low levels of c-sis, the protooncogene coding for the B chain of platelet-derived growth factor, a protein with chemotactic and mitogenic activity toward mesenchymal cells. We therefore hypothesized that alveolar macrophages in patients with idiopathic pulmonary fibrosis may release increased amounts of platelet-derived growth factor, which might help to explain the accumulation of mesenchymal cells and the fibrosis of the lower respiratory tract in the disease. Evaluation of alveolar macrophages recovered from the lungs of patients with idiopathic pulmonary fibrosis demonstrated that these cells spontaneously released four times more platelet-derived growth factor than did alveolar macrophages recovered from normal persons (P less than 0.01). That the platelet-derived growth factor molecules were potentially active was shown by their chemotactic activity for smooth-muscle cells and their ability to act as a "competence" factor for fibroblast growth. These observations suggest the possibility that the accumulation of mesenchymal cells within the alveolar walls in patients with idiopathic pulmonary fibrosis may result partly from the exaggerated release of the potent mitogen platelet-derived growth factor by mononuclear phagocytes in the lower respiratory tract.
Development of Proteomic Patterns for Detecting Lung Cancer (2003)

Lung cancer is at present the number one cause of cancer death and no biomarker is available to detect early lung cancer in serum samples so far. The objective of this study is to find specific biomarkers for detection of lung cancer using Surface Enhanced Laser Desorption/Ionization (SELDI) technology. In this study, serum samples from 30 lung cancer patients and 51 age‐and sex‐matched healthy were analyzed by SELDI based ProteinChip reader, PBSII‐C. The spectra were generated on WCX2 chips and protein peaks clustering and classification analyses were performed utilizing Biomarker Wizard and Biomarker Patterns software packages, respectively. Three protein peaks were automatically chosen for the system training and the development of a decision classification tree. The constructed model was then used to test an independent set of masked serum samples from 15 lung cancer patients and 31 healthy individuals. The analysis yielded a sensitivity of 93.3%, and a specificity of 96.7%. These results suggest that the serum is a capable resource for detection of specific lung cancer biomarkers. SELDI technique combined with an artificial intelligence classification algorithm can both facilitate the discovery of better biomarkers for lung cancer and provide a useful tool for molecular diagnosis in future.
Long Non-Coding RNA Targeting and Transcriptional De-Repression (2013)

Our current understanding of the molecular events that functionally characterize cellular biology continues to be revised. Recent observations find that the vast majority of the human genome is transcribed and may be functionally relevant. Many of these previously unrecognized transcripts, both short and long non-coding RNAs, have been found to be active modulators of protein coding gene function. While such observations were in the past relegated to imprinted genes, it is now becoming apparent that several different genes in differentiated cells may be under some form of non-coding RNA based regulatory control. Emerging evidence suggests that some of these long non-coding RNAs are functional in controlling gene transcription by the targeted recruitment of epigenetic silencing complexes to homology-containing loci in the genome. Most notably when these repressor non-coding RNAs are targeted using small RNA-based inhibitors (such as with RNA interference), a de-repression of the targeted gene can occur resulting in activation of gene expression. Knowledge of this emerging RNA based epigenetic regulatory network has implications not only in cellular evolution but also for the development of an entirely new area of pharmacology.
Lactoferrin gene expression and regulation: an overview (2002)

Lactoferrin is highly conserved among human, mouse, bovine, and porcine species. The numbers of amino acids encoded by 15 of the 17 exons in these species are identical, and in 12 locations, they have identical codon interruptions at the intron-exon splice junctions. However, lactoferrin expression is both ubiquitous and species, tissue, and cell-type specific. It is differentially regulated through multiple signaling pathways such as steroid hormone, growth factor, and kinase cascade pathways. Comparing the lactoferrin gene promoters from different species, common and different characteristics are observed. The human, mouse, bovine, porcine, and bubaline (African antelope) promoters all contain a noncanonical TATA box with an adjacent Sp1 site. Both human and mouse have multiple steroid hormone response elements, while none are found in the other species studied, suggesting that the lactoferrin gene is differentially regulated among different species by steroid hormones. Several transcription factors have been identified that are crucial for the expression of the lactoferrin gene during differentiation of the myeloid cells and in estrogen and epidermal growth factor regulation. This article provides an overview on lactoferrin expression and regulation in different species.
Isolation of seven respiratory viruses in shell vials: a practical and highly sensitive method (1993)

The isolation of respiratory viruses in shell vials was compared with isolation in tube cultures in order to determine the sensitivity of the former, rapid method. Twenty of 21 influenza virus and 15 of 15 parainfluenza virus isolates were recovered in shell vials. One hundred twenty-seven of 138 respiratory syncytial virus isolates were detected in shell vials, but only 10 of 21 adenovirus isolates were positive by the rapid method. Shell vials are very effective for the diagnosis of respiratory viral infections, except for those caused by adenovirus.
Biological and Clinical Implications of Comorbidities in Parkinson’s Disease (2017)

A wide spectrum of comorbidities has been associated with Parkinson's disease (PD), a progressive neurodegenerative disease that affects more than seven million people worldwide. Emerging evidence indicates that chronic diseases including diabetes, depression, anemia and cancer may be implicated in the pathogenesis and progression of PD. Recent epidemiological studies suggest that some of these comorbidities may increase the risk of PD and precede the onset of motor symptoms. Further, drugs to treat diabetes and cancer have elicited neuroprotective effects in PD models. Nonetheless, the mechanisms underlying the occurrence of these comorbidities remain elusive. Herein, we discuss the biological and clinical implications of comorbidities in the pathogenesis, progression, and clinical management, with an emphasis on personalized medicine applications for PD.
Characterization of host‐range and cell entry properties of the major genotypes and subtypes of hepatitis C virus† (2005)

Because of the lack of a robust cell culture system, relatively little is known about the molecular details of the cell entry mechanism for hepatitis C virus (HCV). Recently, we described infectious HCV pseudo-particles (HCVpp) that were generated by incorporating unmodified HCV E1E2 glycoproteins into the membrane of retroviral core particles. These initial studies, performed with E1E2 glycoproteins of genotype 1, noted that HCVpp closely mimic the cell entry and neutralization properties of parental HCV. Because sequence variations in E1 and E2 may account for differences in tropism, replication properties, neutralization, and response to treatment in patients infected with different genotypes, we investigated the functional properties of HCV envelope glycoproteins from different genotypes/subtypes. Our studies indicate that hepatocytes were preferential targets of infection in vitro, although HCV replication in extrahepatic sites has been reported in vivo. Receptor competition assays using antibodies against the CD81 ectodomain as well as ectopic expression of CD81 in CD81-deficient HepG2 cells indicated that CD81 is used by all the different genotypes/subtypes analyzed to enter the cells. However, by silencing RNA (siRNA) interference assays, our results show that the level of Scavenger Receptor Class-B Type-I (SR-BI) needed for efficient infection varies between genotypes and subtypes. Finally, sera from chronic HCV carriers were found to exhibit broadly reactive activities that inhibited HCVpp cell entry, but failed to neutralize all the different genotypes. In conclusion, we characterize common steps in the cell entry pathways of the major HCV genotypes that should provide clues for the development of cell entry inhibitors and vaccines.
Quick fmllr for speaker adaptation in speech recognition (2008)

Feature space maximum likelihood linear regression (fMLLR) is a widely used technique for speaker adaptation in HMM-based speech recognition. However, in extremely resource constrained systems the time required to perform the sufficient statistics accumulation for fMLLR adaptation can be considerable. In this paper we describe a novel method that can lead to significant reduction in the time taken for statistics accumulation while preserving the adaptation gains. The proposed quick fMLLR (Q-fMLLR) algorithm is implemented in a state-of-the-art large-vocabulary continuous speech recognition system, and evaluated on a broadcast transcription task. We present results both in terms of the average likelihood after adaptation and the character error rate. It is shown that Q-fMLLR attains the performance of regular fMLLR with a fraction of the computation.
Characterization of frequency conversion crystals for the implementation of a 1-THz bandwidth on the OMEGA laser (2000)

Summary form only given.Direct-drive inertial confinement fusion requires high degree of laser-irradiation uniformity on target. This is being accomplished on the OMEGA laser using beam smoothing by spectral dispersion. Realization of this scheme requires a large spectral bandwidth on the laser driver beams, which are generated at the third harmonic (351 nm) of the Nd:glass laser wavelength. This paper reports on the characterization and implementation of the frequency conversion cells. This is accomplished using an off-line experimental station on which each of the three crystals is prealigned to precise orientations. The cell alignment is confirmed on the experimental station by comparison with calculations. The cell is then mounted on the OMEGA system, adjusted for the different ambient temperature, and again checked against predictions.
Rat carotid neointimal smooth muscle cells reexpress a developmentally regulated mRNA phenotype during repair of arterial injury. (1992)

Smooth muscle cells (SMCs) cultured from the neointima of injured rat carotid arteries have a different shape and organization in vitro than SMCs from the uninjured media. The morphology of neointimal SMCs from adult rats strongly resembles that of a subset of medial SMCs from 12-day-old rat pups. In the present study, we show that adult carotid neointimal SMCs in vitro express the platelet-derived growth factor (PDGF)-B gene but have little or no PDGF alpha-receptor mRNA. In contrast, medial SMCs from contralateral uninjured carotids, grown and passaged under identical conditions, contain abundant PDGF alpha-receptor mRNA but little or no PDGF-B mRNA. Transcript levels for PDGF-A or PDGF beta-receptor were not different in neointimal versus medial SMC cultures. The PDGF mRNA phenotype of adult neointimal SMCs strongly resembles that of an aortic medial SMC subset from newborn rat pups. Although intriguing, the differences in SMC phenotypes we observed in cell culture may depend on unique conditions in vitro and do not necessarily mean that analogous SMC diversity also exists in vivo. To address this question, we constructed and screened a SMC cDNA library for additional molecular markers of the common "pup-intimal" SMC phenotype. Two cDNA clones were identified whose cognate mRNA levels were developmentally regulated in rat aorta in vivo and were present at high levels in the adult carotid neointima formed 2 weeks after balloon catheter injury. Importantly, elevated levels of these two cognate mRNAs in carotid neointima compared with underlying media were maintained in cultures of neointimal versus medial SMCs in vitro. DNA sequence analysis indicated that the cDNA clones encoded rat tropoelastin and alpha 1 procollagen (type I). These results provide further evidence that neointima formation in the adult rat carotid artery depends on reexpression of an SMC phenotype or subpopulation with special properties characteristic of earlier stages of artery wall development. Our studies to date indicate that two of these special properties are paracrine growth factor production and extracellular matrix synthesis.
Characterization of sleep spindles using higher order statistics and spectra (2000)

This work characterizes the dynamics of sleep spindles, observed in electroencephalogram (EEG) recorded from humans during sleep, using both time and frequency domain methods which depend on higher order statistics and spectra. The time domain method combines the use of second- and third-order correlations to reveal information on the stationarity of periodic spindle rhythms to detect transitions between multiple activities. The frequency domain method, based on normalized spectrum and bispectrum, describes frequency interactions associated with nonlinearities occurring in the observed EEG.
Gallium Nitride Based Logpile Photonic Crystals (2011)

We demonstrate a nine-layer logpile three-dimensional photonic crystal (3DPC) composed of single crystalline gallium nitride (GaN) nanorods, ∼100 nm in size with lattice constants of 260, 280, and 300 nm with photonic band gap in the visible region. This unique GaN structure is created through a combined approach of a layer-by-layer template fabrication technique and selective metal organic chemical vapor deposition (MOCVD). These GaN 3DPC exhibit a stacking direction band gap characterized by strong optical reflectance between 380 and 500 nm. By introducing a "line-defect" cavity in the fifth (middle) layer of the 3DPC, a localized transmission mode with a quality factor of 25-30 is also observed within the photonic band gap. The realization of a group III nitride 3DPC with uniform features and a band gap at wavelengths in the visible region is an important step toward realizing complete control of the electromagnetic environment for group III nitride based optoelectronic devices.