gebhart/patrepeval huggingface dataset:
Sequential expression of vascular endothelial growth factor, Flt-1, and KDR/Flk-1 in regenerating mouse skeletal muscle (2006)

We investigated the expression of vascular endothelial growth factor (VEGF) and its receptors (Flt-1 and KDR/Flk-1) during muscle regeneration by immunohistochemistry and real-time RT-PCR. On days 5 and 7 after the induction of injury, VEGF and Flt-1 were detected in the cytoplasm and KDR/Flk-1 in the cytoplasm and on cell membranes of the same regenerating muscle fibers. The levels of these proteins in the regenerating muscle fibers gradually decreased until day 20. In contrast, these proteins were not detected in the fibers of normal muscle. This suggests that regenerating muscle fibers express VEGF and its receptors in response to injury. In addition, we found that the VEGF mRNA transcript transiently increased after 12 h of muscle injury and then returned to the basal levels observed in normal muscles on day 1. The expression of Flt-1 and KDR/Flk-1 mRNA transcripts also peaked on day 3 and then returned to the basal levels observed in normal muscles on day 10. These findings suggest that regenerating muscle fibers are an important source of VEGF and that VEGF signaling through Flt-1 and KDR/Flk-1 may be involved in the process of muscle regeneration in vivo.
Road crack detection using deep convolutional neural network (2016)

Automatic detection of pavement cracks is an important task in transportation maintenance for driving safety assurance. However, it remains a challenging task due to the intensity inhomogeneity of cracks and complexity of the background, e.g., the low contrast with surrounding pavement and possible shadows with similar intensity. Inspired by recent success on applying deep learning to computer vision and medical problems, a deep-learning based method for crack detection is proposed in this paper. A supervised deep convolutional neural network is trained to classify each image patch in the collected images. Quantitative evaluation conducted on a data set of 500 images of size 3264 χ 2448, collected by a low-cost smart phone, demonstrates that the learned deep features with the proposed deep learning framework provide superior crack detection performance when compared with features extracted with existing hand-craft methods.
Binding of Mismatched Microsatellite DNA Sequences by the Human MSH2 Protein (1994)

Alteration of the human mismatch repair gene hMSH2 has been linked to the microsatellite DNA instability found in hereditary nonpolyposis colon cancer and several sporadic cancers. This microsatellite DNA instability is thought to arise from defective repair of DNA replication errors that create insertion-deletion loop-type (IDL) mismatched nucleotides. Here, it is shown that purified hMSH2 protein efficiently and specifically binds DNA containing IDL mismatches of up to 14 nucleotides. These results support a direct role for hMSH2 in mutation avoidance and microsatellite stability in human cells.
Intelligent control techniques for humanoid robots (2003)

This paper focuses on the application of the intelligent control techniques (neural networks, fuzzy logic and genetic algorithms) and their hybrid methods (neuro-fuzzy networks, neuro-genetic and fuzzy-genetic algorithms) in the area of humanoid robotic systems. This paper represents an attempt to give a report of the basic principles and concepts of intelligent control in humanoid robotics, with an outline of a number of recent algorithms used in advanced control of humanoid robots.
Molecules in a Bose-Einstein Condensate (2000)

State-selected rubidium-87 molecules were created at rest in a dilute Bose-Einstein condensate of rubidium-87 atoms with coherent free-bound stimulated Raman transitions. The transition rate exhibited a resonance line shape with an extremely narrow width as small as 1.5 kilohertz. The precise shape and position of the resonance are sensitive to the mean-field interactions between the molecules and the atomic condensate. As a result, we were able to measure the molecule-condensate interactions. This method allows molecular binding energies to be determined with unprecedented accuracy and is of interest as a mechanism for the generation of a molecular Bose-Einstein condensate.
Methods and Applications of Three-Color Confocal Imaging (1997)

A simple method for constructing two- and three-color merged images from grayscale confocal fluorescence images using Adobe Photoshop is outlined. Various computer methods for manipulating and displaying the images are discussed in light of several recent biomedical applications of multi-label confocal microscopy.
Neurochemistry of dementia: establishing the links. (1989)

Neurochemical research in dementia needs to move beyond descriptive inventories of neurotransmitter systems affected in the specific disorders and to link to molecular studies of mechanism and clinical studies of cognition. New advances in Alzheimer's Disease (AD), Huntington's Disease (HD), and Parkinson's Disease (PD) are being guided by models of how nerve cells die in these disorders. Theories of pathophysiology which address the cellular level need to explain the selective vulnerability of neuronal populations in the different diseases. Clinically, the importance of neurochemical studies will be increased by understanding the bridges between neural and cognitive processes. Clinicians are concerned about the nosology of dementias, diagnostic tests, and more effective therapies. The value of neurochemical studies will be enhanced to the extent that they can contribute to understanding and modifying the clinical phenomenology of these disorders. In this paper, we will briefly review what is known about the neurochemistry of dementia but focus most of our attention on establishing the linkage between this level of description and the levels of description which are either "downstream" (molecular biology) or "upstream" (cognition) in terms of a reductionistic conception of understanding the disease process. We will explore how understanding neurochemistry relates to our understanding of disease mechanism and what constraints neurochemical studies place on understanding clinical aspects of disease. We will conclude by briefly discussing some of the problems with our current understanding of the neurochemistry of dementia and how we can address those problems in the future.
The transglutaminase in vascular cells and tissues could provide an alternate pathway for fibrin stabilization (1987)

Abstract A thrombin-independent transglutaminase (TG) has been identified in vascular cells and tissues from human, rabbit, rat, porcine, and bovine sources. The vascular TG had several properties that were similar but not identical to guinea pig liver TG. Both enzymes had similar chromatographic and electrophoretic properties, preferentially cross- linked the alpha-chains of fibrinogen, and reacted with polyclonal and monoclonal anti-guinea-pig liver TG antibodies. However, the TG from adult bovine aortic endothelial (ABAE) cells exhibited a novel Ca2+/Mg2+ dependence for enzymatic activity that was distinct from that of purified guinea pig liver TG. The mol wt of the vascular TG (79 +/- 3 kd) determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) was slightly lower than the purified guinea pig liver TG (85 +/- 9 kd). The TG antigen was detected by immunohistochemical techniques in association with the endothelial and smooth muscle cells of arteries, veins, venules, and capillaries. The TG antigen also codistributed with the fibronectin antigen along the hepatic sinusoids. The ABAE cell TG cross-linked alpha 2-plasmin inhibitor to fibrinogen and caused the modified fibrinogen to be 40- fold more resistant to plasminolysis. A thrombin-independent TG in vascular cells of blood vessels could provide an alternate pathway to inhibit fibrinolysis and promote fibrin stabilization.
Vietnam - Transmission and Distribution Development Project - environmental impact analysis (2003)

This is an environmental assessment for Vietnam's Transmission and Distribution Development Project, in which the Playcu-Phulam transmission line integrates small and medium power generation, such as linking hydropower in the western highlands with the rest of the country. Transmission lines will help create a reliable, economical power supply in the South. Construction activities such as cutting trees, clearing routes, digging foundation holes, transporting material, and tensioning conductors can cause soil erosion. Mitigating options include soil replacing, and tree and grass planting. To offset hunting and poaching, fences will be erected and foresty controllers will increase their supervision and inspections. To prevent fire or explosion caused by hazardous spills, construction crews will be supplied protection equipment. To reduce disease risk in construction camps, medical and hygienic measures for handling water and foodstuffs will be firmly adhered to. During the operational phase, the threat of soil erosion around the towers can be alleviated by building a foundation embankment or contouring on sloping land. Trees posing a safety hazard because they are too close to transmission lines will be cut down periodically. A resettlement action plan recommends solutions for compensation, population relocation, and household restoration.
Nonspecific Interactions of a Carboxylate-Substituted PPE with Proteins. A Cautionary Tale for Biosensor Applications (2005)

Two carboxylate-substituted, fluorescent (Phi = 0.08), water-soluble poly(p-phenyleneethynylene)s (PPE) and a water-soluble model compound were exposed to a series of proteins and bovine serum. While the anionic PPEs do not have any specific binding sites, they form stable complexes with histone, lysozyme, myoglobin, and hemoglobin. The complex formation was evidenced by fluorescence quenching. Bovine serum albumin does not quench the fluorescence of the PPEs but enhances it, probably due to its surfactant character. These results imply that the use of charged conjugated polymers as biosensors, while an attractive proposition, has to take into account strong nonspecific interactions between conjugated polymers and the host of proteins that is found in cells and complex biological fluids.
Stable Expression of Recombinant Factor VIII Molecules Using a Bovine Papillomavirus Vector (1987)

The bleeding disorder in hemophilia A results from a deficiency or abnormality of Factor VIII (FVIII), a member of the coagulation cascade. FVIII is a large glycoprotein (approximately 350,000 daltons) that is activated by a series of proteolytic cleavages. During activation, a large internal domain (B domain) is removed, resulting in an active complex comprised of the amino and carboxyl subunits of the parental molecule. Using a bovine papillomavirus expression vector system, we have established stable, genetically engineered cell lines harboring either full-length FVIII cDNA or variant FVIII cDNA (delta FVIII), the latter containing an extensive deletion in the region encoding the B domain. We demonstrate that the two recombinant FVIII molecules manifest the biological attributes of native FVIII. Relative to full-length FVIII transformants, cells harboring delta FVIII cDNA are five to eight times more efficient in expressing coagulant activity. This difference is due to a post-transcriptional event.
F-T-LSTM Based Complex Network for Joint Acoustic Echo Cancellation and Speech Enhancement (2021)

With the increasing demand for audio communication and online conference, ensuring the robustness of Acoustic Echo Cancellation (AEC) under the complicated acoustic scenario including noise, reverberation and nonlinear distortion has become a top issue. Although there have been some traditional methods that consider nonlinear distortion, they are still inefficient for echo suppression and the performance will be attenuated when noise is present. In this paper, we present a real-time AEC approach using complex neural network to better modeling the important phase information and frequency-time-LSTMs (F-T-LSTM), which scan both frequency and time axis, for better temporal modeling. Moreover, we utilize modified SI-SNR as cost function to make the model to have better echo cancellation and noise suppression (NS) performance. With only 1.4M parameters, the proposed approach outperforms the AEC-challenge baseline by 0.27 in terms of Mean Opinion Score (MOS).
An Update on Photodynamic Therapy Applications (2002)

Photodynamic therapy (PDT), following health agency approvals throughout the world for various cancers and other diseases, is slowly being accepted as a standard treatment to be added to the medical practitioner's armamentarium. This includes palliative treatments such as for obstructive esophageal and lung cancers as well as those intended for cure, early stage lung cancer, and actinic keratoses. A particularly new and important application is for the treatment of age-related macular degeneration (AMD), where PDT (Visudyne) has made a major impact on the outcome of this disease, the major cause of blindness in those over the age of 50. In the cancer field, while not yet approved (pending), the use of PDT in treatment of high-grade dysplasia (HGD) in Barrett's esophagus may well change how this disease is currently treated (often esophagectomy). Mechanistically, the recognition of apoptosis as an important mode of cell death following PDT and the critical role of the inflammatory process and immunity has only recently been recognized. This review updates the current and future role of PDT in cancer and other diseases.
[Study on the processing of leech by FTIR and 2D-IR correlation spectroscopy]. (2011)

The chemical differences of traditional Chinese medicine leech before and after processing were analyzed by FTIR and two-dimensional correlation infrared (2D-IR) spectroscopy. The result showed that the leech was high in protein, with characteristic peaks of amide I, II bands. Comparing the IR spectra of samples, the primary difference was that the characteristic peak of fresh leech was at 1 543 cm(-1), while that of crude and processed leech was at 1 535 cm(-1). A 2D-IR spectrum with heating perturbation was used to track the processing dynamics of leech In the 2D-IR correlation spectra, fresh leech exhibited stronger automatic peaks of the amide I and II bands than that of processed leech, which indicates that the protein components of the fresh leech were more sensitive to heat perturbation than the processed one. Moreover, the result of FTIR and 2D-IR correlation spectra validated that the 3-dimensional structure of protein was damaged and hydrogen bonds were broken after processing, which resulted in the inactivation of protein. The fatty acids and cholesterol components of leech were also oxidized in this process.
Antiinflammatory activity of a COOH-terminal fragment of the neuropeptide alpha-MSH. (1989)

The endogenous neuropeptide alpha-melanocyte stimulating hormone (alpha-MSH 1-13), previously found to have marked antipyretic activity, inhibits histamine-induced increases in vasopermeability. The primary antipyretic amino acid message sequence is believed to be the COOH-terminal trieptide, lysine-proline-valine. In recent preliminary research this tripeptide inhibited increases in vasopermeability, raising the possibility that this portion of the alpha-MSH molecule has general antiinflammatory activity. To test this idea, the effects of graded doses of alpha-MSH [11-13] on ear swelling induced by picryl chloride in mice were compared with the effects of saline and a large dose of corticosteroid. Alpha-MSH [11-13] inhibited swelling in a dose-related fashion. This result, together with previous findings, suggests that endogenous circulating alpha-MSH and its COOH-terminal fragments may contribute to modulation of physiological responses in host defense. If this is true, it may be possible to develop new peptide drugs or mimetics based on the tripeptide that are useful in treating inflammation.
SHP-1 Binds and Negatively Modulates the c-Kit Receptor by Interaction with Tyrosine 569 in the c-Kit Juxtamembrane Domain (1998)

The SH2 domain-containing SHP-1 tyrosine phosphatase has been shown to negatively regulate a broad spectrum of growth factor- and cytokine-driven mitogenic signaling pathways. Included among these is the cascade of intracellular events evoked by stem cell factor binding to c-Kit, a tyrosine kinase receptor which associates with and is dephosphorylated by SHP-1. Using a series of glutathione S-transferase (GST) fusion proteins containing either tyrosine-phosphorylated segments of the c-Kit cytosolic region or the SH2 domains of SHP-1, we have shown that SHP-1 interacts with c-Kit by binding selectively to the phosphorylated c-Kit juxtamembrane region and that the association of c-Kit with the larger of the two SHP-1 isoforms may be mediated through either the N-terminal or C-terminal SHP-1 SH2 domain. The results of binding assays with mutagenized GST-Kit juxtamembrane fusion proteins and competitive inhibition assays with phosphopeptides encompassing each c-Kit juxtamembrane region identified the tyrosine residue at position 569 as the major site for binding of SHP-1 to c-Kit and suggested that tyrosine 567 contributes to, but is not required for, this interaction. By analysis of Ba/F3 cells retrovirally transduced to express c-Kit receptors, phenylalanine substitution of c-Kit tyrosine residue 569 was shown to be associated with disruption of c-Kit-SHP-1 binding and induction of hyperproliferative responses to stem cell factor. Although phenylalanine substitution of c-Kit tyrosine residue 567 in the Ba/F3-c-Kit cells did not alter SHP-1 binding to c-Kit, the capacity of a second c-Kit-binding tyrosine phosphatase, SHP-2, to associate with c-Kit was markedly reduced, and the cells again showed hyperproliferative responses to stem cell factor. These data therefore identify SHP-1 binding to tyrosine 569 on c-Kit as an interaction pivotal to SHP-1 inhibitory effects on c-Kit signaling, but they indicate as well that cytosolic protein tyrosine phosphatases other than SHP-1 may also negatively regulate the coupling of c-Kit engagement to proliferation.
Loss of Hepatocyte-Nuclear-Factor-4α Affects Colonic Ion Transport and Causes Chronic Inflammation Resembling Inflammatory Bowel Disease in Mice (2009)

Our results highlight the critical role of Hnf4alpha to maintain intestinal inflammatory homeostasis during mouse adult life and uncover a novel function for Hnf4alpha in the regulation of claudin-15 expression. This establishes Hnf4alpha as a mediator of ion epithelial transport, an important process for the maintenance of gut inflammatory homeostasis.
Antitumor activity of novel octalactin A analogs in murine leukemia cells in vitro. (1998)

Octalactin A and B (code names K1 and K2) are eight-membered-ring lactones from a marine bacterium. K1 is reportedly cytotoxic. Since access to this natural product is severely limited, the entire synthesis of K1 has been achieved in K. Buszek's laboratory, and several of its structural and stereochemical analogs (code names K3-K9) have been tested for their ability to prevent murine L1210 leukemic cells from synthesizing macromolecules and growing in vitro. At 50 microM, K1 is inactive and the eight-membered lactone K4, an oxocene, is the only compound found to inhibit tumor cell growth by about 90% in the L1210 system. The long-term inhibition of L1210 cell growth by K4 is concentration dependent (IC50 around 10 microM) and not reversible following drug removal. The delayed and weaker cytotoxic effects of K4 suggest that the inhibition of tumor cell proliferation observed 1-4 days after K4 treatment is not solely caused by drug cytotoxicity. When compared to a spectrum of representative anticancer drugs, higher concentrations of K4 must be used to maximally inhibit tumor cell growth. In contrast to its antiproliferative activity, 50 microM K4 fails to alter the rates of DNA, RNA and protein synthesis in L1210 cells. This discrepancy between the ability of K4 to inhibit macromolecule synthesis and leukemic cell growth suggests that other molecular targets are involved in the antitumor action of this drug. At 50 microM, K4 inhibits the polymerization of purified tubulin by about 45%, and therefore may be a novel microtubule de-stabilizing drug weaker than vincristine. Even though other mechanisms may be involved in its antitumor action, the ability of K4 to partially disrupt microtubule dynamics indirectly suggests that this synthetic oxocene may be a cell cycle-specific anticancer drug that blocks mammalian cells in M-phase.
Antisense strategies and non-viral gene therapy for cancer (2002)

Effective gene therapy for cancer remains an elusive goal, even after more than a decade of intensive research. There has been, however, tremendous progress in the development of increasingly sophisticated non-viral (or synthetic) delivery vectors for local and systemic administration of nucleic acids. Recent clinical data has also indicated the feasibility of using antisense oligonucleotides to inhibit inappropriately expressed or mutated genes in human cancers. The purpose of this review is to provide an update of the patent literature on the development of non-viral approaches for cancer gene therapy. In particular, patents on lipoplexes and polyplexes for delivery of therapeutic genes and antisense oligonucleotides are reviewed. The diverse range of antisense strategies being developed and recent clinical data are also highlighted.
Mixotrophic cultivation of Chlorella vulgaris using industrial dairy waste as organic carbon source (2012)

Growth parameters and biochemical composition of the green microalga Chlorella vulgaris cultivated under different mixotrophic conditions were determined and compared to those obtained from a photoautotrophic control culture. Mixotrophic microalgae showed higher specific growth rate, final biomass concentration and productivities of lipids, starch and proteins than microalgae cultivated under photoautotrophic conditions. Moreover, supplementation of the inorganic culture medium with hydrolyzed cheese whey powder solution led to a significant improvement in microalgal biomass production and carbohydrate utilization when compared with the culture enriched with a mixture of pure glucose and galactose, due to the presence of growth promoting nutrients in cheese whey. Mixotrophic cultivation of C. vulgaris using the main dairy industry by-product could be considered a feasible alternative to reduce the costs of microalgal biomass production, since it does not require the addition of expensive carbohydrates to the culture medium.
Metal Binding Modes of Alzheimer's Amyloid β-Peptide in Insoluble Aggregates and Soluble Complexes (2000)

Aggregation of the amyloid beta-peptide (Abeta) into insoluble fibrils is a key pathological event in Alzheimer's disease. Zn(II) induces the Abeta aggregation at acidic-to-neutral pH, while Cu(II) is an effective inducer only at mildly acidic pH. We have examined Zn(II) and Cu(II) binding modes of Abeta and their pH dependence by Raman spectroscopy. The Raman spectra clearly demonstrate that three histidine residues in the N-terminal hydrophilic region provide primary metal binding sites and the solubility of the metal-Abeta complex is correlated with the metal binding mode. Zn(II) binds to the N(tau) atom of the histidine imidazole ring and the peptide aggregates through intermolecular His(N(tau))-Zn(II)-His(N(tau)) bridges. The N(tau)-metal ligation also occurs in Cu(II)-induced Abeta aggregation at mildly acidic pH. At neutral pH, however, Cu(II) binds to N(pi), the other nitrogen of the histidine imidazole ring, and to deprotonated amide nitrogens of the peptide main chain. The chelation of Cu(II) by histidine and main-chain amide groups results in soluble Cu(II)-Abeta complexes. Under normal physiological conditions, Cu(II) is expected to protect Abeta against Zn(II)-induced aggregation by competing with Zn(II) for histidine residues of Abeta.